Jericho signed a contract with the World Wrestling Federation (WWF) on June 30, 1999. In the weeks before Jericho's debut, a clock labelled "countdown to the new millennium" appeared on WWF programming. The clock finally ran down on the August 9, 1999 episode of Raw, in Chicago, Illinois. Whilst The Rock was in the ring cutting a promo on the Big Show, Jericho entered the arena and proclaimed "Raw is Jericho" and that he had "come to save the World Wrestling Federation", referring to himself as "Y2J" (a play on the Y2K bug). The Rock proceeded to verbally mock him for his interruption. Later that month, Jericho made his in-ring debut on August 26, 1999, losing by disqualification in a match against Road Dogg on the inaugural episode of SmackDown! after powerbombing Road Dogg through a table.
Jericho's first long-term feud was with Chyna, for the Intercontinental Championship. After losing to Chyna at the Survivor Series, Jericho won his first Intercontinental title at Armageddon. This feud included a controversial decision during a rematch in which two separate referees declared each one of them the winner of a match for the title. As a result, they became co-owners of the title until Jericho attained sole ownership at the Royal Rumble. Jericho's subsequent alliance with Chyna, coupled with growing enthusiasm for his ring work and mic skills, effectively turned him into a face.
Jericho lost his title to the European Champion Kurt Angle at No Way Out. On April 2, Jericho competed in a Triple Threat match against Chris Benoit and Angle at WrestleMania 2000 in a two-falls contest with both of Angle's titles at stake. Jericho won the European Championship by pinning Benoit, who in turn pinned Jericho to take the Intercontinental Championship. This was the first of six pay-per-view matches between the pair within twelve months. Jericho lost the title the next day to Eddie Guerrero on Raw after Chyna turned heel to side with Guerrero. On the April 17 episode of Raw, Jericho upset Triple H in a WWF Championship match. Referee Earl Hebner made a fast count when Jericho pinned Triple H, causing Jericho to win the title. Hebner later reversed the decision due to pressure from Triple H, and WWE does not recognize Jericho's reign as champion. On the May 4 episode of SmackDown!, Jericho defeated Benoit to become Intercontinental Champion for the third time, but lost the title to Benoit four days later on Raw. Meanwhile, Jericho's feud with Triple H climaxed at Fully Loaded, when they competed in a Last Man Standing match. Jericho lost the match to Triple H only by one second, despite the repeated assistance Triple H's wife, Stephanie, provided him in the match.
At the 2001 Royal Rumble, Jericho defeated Chris Benoit in a Ladder match to win the Intercontinental Championship for the fourth time. At WrestleMania X-Seven, he successfully defended his title in a match against William Regal, only to lose it four days later to Triple H.
At Judgment Day, Jericho and Benoit won a Tag Team Turmoil match and earned a shot at Stone Cold Steve Austin and Triple H for their WWF Tag Team Championship on Raw the next night. Benoit and Jericho won the match, in which Triple H legitimately tore his quadriceps and would spend the rest of the year injured. Benoit and Jericho each became a WWF Tag Team Champion for the first time. The team defended their title in the first Fatal Four-Way Tables, Ladders, and Chairs match where Benoit sustained a year-long injury doing a diving headbutt through a table. Though Benoit was carried out on a stretcher, he returned to the match to climb the ladder and retain the championship. The duo lost the title one month later to the Dudley Boyz on June 19, 2001. That month at King of the Ring, both Benoit and Jericho were named challengers for Austin's WWF Championship in which Booker T interfered as the catalyst for The Invasion angle.
In the following months, Jericho became a major force in The Invasion storyline in which the Alliance formed to overtake the WWF. Jericho remained on the side of the WWF, however, Jericho began to show jealousy toward fellow WWF member The Rock. They faced each other in a match at No Mercy for the World Heavyweight Championship after Jericho defeated Rob Van Dam in a number one contenders match. Jericho won the World Heavyweight Championship when he pinned The Rock after debuting a new finisher, the Breakdown. One night later, the two put their differences aside and won the WWF Tag Team title from the Dudley Boyz. After they lost the title to Test and Booker T, they continued their feud. On the November 5 episode of Raw, The Rock defeated Jericho to regain the championship. Following the match, Jericho attacked The Rock with a steel chair. At the Survivor Series, Jericho almost cost The Rock, and the WWF, victory in their elimination matchup by attacking The Rock again, turning heel once again. On December 9, at Vengeance, Jericho defeated both The Rock for the World Heavyweight Championship and Stone Cold Steve Austin for his WWF Championship on the same night to become the first wrestler to hold both championships at the same time, which made him the first Undisputed WWF Champion. He fought both of the men he defeated at Vengeance on separate occasions and retained his title at the next two pay-per-views, Royal Rumble (vs. The Rock) and No Way Out (vs. Stone Cold). Jericho later lost the title to Triple H in the main event of WrestleMania X8. After his title loss, Jericho became a member of the SmackDown! roster and continued his feud with Triple H. The rivalry culminated at Judgment Day when Triple H defeated Jericho in a Hell in a Cell match.
Jericho was later drafted to Raw, where he won the Intercontinental Championship from Rob Van Dam (RVD). He then later formed a tag team with Christian, with whom he won the World Tag Team Championship, on October 14, 2002. Christian and Jericho lost the title in a fatal four-way elimination match, involving the teams of The Dudley Boyz, Booker T and Goldust, and William Regal and Lance Storm, on December 15, 2002 at Armageddon.
On January 13, 2003, Jericho won an over-the-top-rope challenge against Kane, RVD, and Batista to select his entry number for the Royal Rumble match. He chose number two in order to start the match with Shawn Michaels, who had challenged Jericho to prove his claims that he was better than Michaels. After Michaels' entrance, Jericho entered as the second participant. Christian, in Jericho's attire, appeared while the real Jericho attacked Shawn from behind. He eliminated Michaels shortly afterward, but Michaels got his revenge later in the match by causing Test to eliminate Jericho. Jericho spent the most time of any other wrestler in that same Royal Rumble. Jericho simultaneously feuded with Test, Michaels, and Jeff Hardy. Jericho and Michaels fought again at WrestleMania XIX. In the end, Michaels scored the victory. Jericho, however, hit Michaels with a low blow after the match following an embrace.
After this match, Jericho entered a rivalry with Goldberg. During Jericho's first episode of the Highlight Reel, an interview show, where Goldberg was the guest, he complained that no-one wanted Goldberg in WWE and continued to insult him in the following weeks. On May 12 on Raw, a mystery assailant attempted to run over Goldberg with a limousine. A week later, Co-Raw General Manager, Stone Cold Steve Austin, interrogated several Raw superstars to find out who was driving the car. One of the interrogates was Lance Storm, who admitted that he was the assailant. Austin forced Storm into a match with Goldberg, who defeated Storm. After the match, Goldberg forced Storm to admit that Jericho was the superstar who conspired Storm into running him over. On May 26, Goldberg was once again a guest on the Highlight Reel. Jericho expressed jealousy towards Goldberg's success, and felt that since joining WWE, he had achieved everything he had ever wanted in his career and all that was left was to defeat Goldberg and challenged him to a match. At Bad Blood, Goldberg settled the score with Jericho and defeated him.
Later in 2003, Jericho began a romance with Trish Stratus while his tag team partner Christian began one with Lita. This, however, turned out to be a bet over who could sleep with their respective paramour first, with a Canadian dollar at stake. Stratus overheard this and ended her relationship with Jericho, who seemingly felt bad for using Stratus. After he saved her from an attack by Kane, Stratus agreed that the two of them could just be "friends", thus making Jericho a face. After Christian put Stratus in the Walls of Jericho while competing against her in a match, Jericho sought revenge on Christian, which led to a match at WrestleMania XX. Christian defeated Jericho after Stratus ran down and "inadvertently" struck Jericho (thinking it was Christian) and Christian got the roll-up. After the match, Stratus turned on Jericho and revealed that she and Christian were a couple. This revelation led to a handicap match at Backlash that Jericho won. Jericho won his seventh Intercontinental Championship at that year's Unforgiven in a ladder match against Christian. Jericho's seventh reign was short lived, as he lost it at Taboo Tuesday to Shelton Benjamin.
Jericho teamed up with Randy Orton, Chris Benoit, and Maven to take on Triple H, Batista, Edge, and Snitsky at Survivor Series. The match's stipulation stated that each member of the winning team would become the General Manager of Raw throughout the next four weeks. Jericho's team was victorious, so they took turns as General Manager. During Jericho's turn as General Manager, he stripped Triple H of his World Heavyweight Championship because a Triple Threat match for the title a week earlier ended in a draw. At New Year's Revolution, Jericho competed in the Elimination Chamber against Triple H, Chris Benoit, Batista, Randy Orton, and Edge for the vacated World Heavyweight Championship. Jericho began the match with Benoit but Batista ultimately eliminated Jericho. At WrestleMania 21, Jericho participated in the first ever Money in the Bank ladder match. Jericho suggested the match concept, and he competed in the match against Benjamin, Benoit, Kane, Christian, and Edge. Jericho lost the match when Edge claimed the briefcase. At Backlash, Jericho challenging Shelton Benjamin for the Intercontinental Championship, but lost the match. On June 12, 2005, Jericho wrestled in his first match of the ECW One Night Stand pay-per-view event against Lance Storm. Jericho used his 'Lionheart' gimmick, instead of his more well known 'Y2J' gimmick. However, Jericho lost the match after Justin Credible hit Jericho's head with a Singapore Cane, which allowed Storm to win the match.
Later that June, Jericho turned on WWE Champion John Cena, turned heel once again. Jericho lost a Triple Threat match for the WWE Championship at Vengeance which also involved Christian and Cena. The feud continued throughout the summer and Jericho lost to Cena in a WWE Championship match at SummerSlam. His last appearance in WWE on the next night on the August 22 episode of Raw, Jericho faced Cena again in a rematch, this time in a "You're fired" match. Cena won again, and Jericho was fired by Raw General Manager Eric Bischoff, after the match, Jericho turned on Bischoff. However, Jericho was carried out of the arena by security, Kurt Angle attacked Cena. WWE announced that Jericho's WWE contract had expired on August 25, 2005.
After a two-year hiatus, WWE promoted Jericho's return starting September 24, 2007 with a viral marketing campaign using a series of 15-second cryptic binary code videos. The videos contained hidden messages and biblical links related to Jericho. Jericho made his return to WWE television as a face on the November 19, 2007 episode of Raw when he interrupted Randy Orton during Orton's orchestrated passing of the torch ceremony. Jericho revealed his intentions to reclaim the WWE Championship in order to "save" WWE fans from Orton. On the November 26 episode of Raw, Jericho defeated Santino Marella and debuted a new finishing maneuver called the Codebreaker. At Armageddon, he competed in a WWE title match against Orton, defeating him by disqualification when SmackDown's color commentator John "Bradshaw" Layfield interfered in the match, but Orton retained the title. He began a feud with JBL and met him at the Royal Rumble. Jericho was disqualified after hitting JBL with a steel chair. On the March 10 episode of Raw, Jericho captured the Intercontinental Championship for a record eighth time when he defeated Jeff Hardy.
In April 2008, Jericho became involved in the ongoing feud between Shawn Michaels and Batista when he suggested that Michaels enjoyed retiring Ric Flair, causing Michaels to superkick him. Jericho thus asked to be inserted into Batista's and Michaels' match at Backlash, but instead, he was appointed as the special guest referee. During the match at Backlash, Michaels feigned a knee injury so that Jericho would give him time to recover and sucker Batista in for a superkick for the win. After Backlash, Jericho accused Michaels of cheating, but Michaels continued to play up an injury. When Jericho was finally convinced and he apologized to Michaels for not believing him, Michaels then admitted to Jericho that he had faked his injury and he superkicked Jericho. Michaels then defeated Jericho at Judgment Day, with Jericho initiating a handshake after the match.
On the June 9 episode of Raw, Jericho hosted his talk show segment, The Highlight Reel, interviewing Michaels. Jericho pointed out that Michaels was still cheered by the fans despite Michaels' deceit and attack on Jericho during the previous months, whereas Jericho was booed when he tried to do the right thing. Jericho then assaulted Michaels with a low blow and sent Michaels through the "Jeritron 5000" television, damaging Michaels' eye, thus Jericho turned heel for the first time since 2005. At Night of Champions, Jericho lost the Intercontinental Title to Kofi Kingston after a distraction by Michaels. In June, Jericho also took on Lance Cade as a protegé.
Afterward, Jericho developed a suit-wearing "self righteous honest man" gimmick. Jericho and Michaels met at The Great American Bash, which Jericho won after attacking the cut on Michaels's eye. Michaels later announced that his eye damage would force him to retire, but insulted Jericho that Jericho would never achieve Michaels' success. Jericho went to attack Michaels, but Michaels ducked, causing Jericho's punch to land on Michaels' wife, Rebecca, instead. As a result, they met in an Unsanctioned match at Unforgiven which Jericho lost. In the main event of Unforgiven, Jericho entered the Championship Scramble as a replacement for the defending champion CM Punk and subsequently won the World Heavyweight Championship. Jericho then successfully defended his title against Michaels at No Mercy in a ladder match after Lance Cade interfered. At Cyber Sunday, Jericho lost the title to Batista in a regular match. Eight days later, Jericho defeated Batista to win back the title in a steel cage match. Jericho ended his feud with Michaels by beating Michaels in a Last Man Standing match on the November 10 episode of Raw after interference from John "Bradshaw" Layfield. Jericho's reign as World Champion lasted until the 2008 Survivor Series, where Jericho lost to the returning John Cena.
On the January 12, 2009 episode of Raw, WWE Executive Vice President Stephanie McMahon fired Jericho, but he was rehired the following week after making a forced apology. On February 15 at No Way Out, he was eliminated by Rey Mysterio, while Mysterio was defeated by Edge to become new World Heavyweight Champion.
Jericho had an on-screen feud with film star Mickey Rourke and with four WWE Hall of Famers. He challenged and attacked Ric Flair, Roddy Piper, Jimmy Snuka, and Ricky Steamboat on various episodes of Raw leading to WrestleMania XXV. At the event he won an elimination match against Snuka, Steamboat and Piper. After this, Jericho challenged Rourke who was at ringside for the event. As part of the storyline, Rourke knocked Jericho out after a left hook to the jaw.
On the April 13 episode of Raw, Jericho was drafted to the SmackDown brand as part of the 2009 WWE Draft. Ricky Steamboat interrupted Jericho's Raw farewell address, which led to the two facing off at Backlash where Jericho came out victorious. In his SmackDown return, Jericho participated in a fatal-four-way elimination match against Kane, Jeff Hardy, and Rey Mysterio. Mysterio executed a 619 on Jericho and then attempted to pin him with a seated senton. Jericho retaliated by throwing a chair at Mysterio and was disqualified. This sparked a feud between the two. Mysterio pinned Jericho after a 619 at Judgment Day to retain the Intercontinental Championship. Jericho defeated Mysterio in a No Holds Barred Match at Extreme Rules to win his ninth Intercontinental Championship, breaking his own record again. At The Bash Jericho lost the Intercontinental title to Mysterio.
Later in the same pay-per-view, Jericho and his partner Edge won the Unified Tag Team Championship as surprise entrants in a tag team match. Shortly thereafter Edge suffered an injury and Jericho announced that he had a clause in his contract to allow Edge to be replaced and Jericho's reign to continue uninterrupted. At Night of Champions, Jericho revealed Big Show as his new tag team partner and Jeri-Show defeated Cody Rhodes and Ted DiBiase to retain the championship. Jeri-Show successfully defended their titles against Cryme Tyme at SummerSlam, MVP and Mark Henry at Breaking Point and also Rey Mysterio and Batista at Hell in a Cell. At Survivor Series, both Jericho and Big Show took part in a triple threat match for the World Heavyweight Championship, but The Undertaker successfully retained his title.
At the 2010 Royal Rumble Jericho was eliminated by the returning Edge, his former tag team partner, who went on to win the match. At Elimination Chamber, Jericho won the World Heavyweight Championship in an Elimination Chamber match, defeating The Undertaker following interference from Shawn Michaels. The next night on Raw, Edge announced that he would be using his Royal Rumble win to challenge Jericho at WrestleMania XXVI for the World Heavyweight Championship. Jericho defeated Edge at WrestleMania but during the April 2 episode of SmackDown!, Jack Swagger cashed in his Money in the Bank contract and pinned Jericho for the championship after he had been speared by Edge. Swagger retained the championship in a match against Jericho and Edge soon after. Edge defeated Jericho in a steel cage match at Extreme Rules to end the feud.
Jericho was drafted back to Raw in May's 2010 WWE Draft. He formed a brief tag team with The Miz and unsuccessfully challenged The Hart Dynasty for the Unified Tag Team Championship at Over the Limit. A month later, Jericho lost to Evan Bourne at WWE Fatal 4-Way, and the following night won a rematch where he put his career on the line. On the July 19 episode of Raw, after being assaulted by The Nexus, Jericho began showing signs of a face turn when he teamed with rivals Edge, John Morrison, R-Truth, The Great Khali and Bret Hart in a team led by John Cena to face The Nexus at SummerSlam. Jericho and Cena bickered over leadership of the team, which led to him and Edge attacking Cena during the SummerSlam match that they won.
Jericho was punished for not showing solidarity against Nexus, when he was removed from a Six-Pack Challenge for Sheamus' WWE Championship at WWE Night of Champions. Although he re-earned his place in the match he was the first man eliminated. Following an unscripted backstage interview, Jericho burst into tears and fled from the arena. On the September 27 episode of Raw, Jericho faced Randy Orton who punted him in the head. This was used to explain Jericho's departure from the company.
Beginning in November 2011, WWE aired six cryptic vignettes that implied that someone would be returning to the company during the broadcast of the January 2, 2012 episode of Raw. Jericho returned on the January 2 episode of Raw as a tweener in a similar manner to his two previous WWE introductions; however, after physically hyping the crowd and relishing their cheers for a prolonged period, a smiling Jericho left without verbally addressing his return and did so the following week. On the January 16 episode of Raw, Jericho made his in-ring return in a six-man tag team match, although Jericho had no physical involvement in the match; he hyped the crowd upon tagging in, before tagging out and abandoning the match. Jericho finally spoke the following week to say, "This Sunday at the Royal Rumble, it is going to be the end of the world as you know it", but in the Royal Rumble match, he was eliminated last, by Sheamus.
On the January 30 episode of Raw, Jericho interfered in a match between WWE Champion CM Punk and World Heavyweight Champion Daniel Bryan, causing a disqualification victory for Bryan and then attacking Punk following the ruling. The following week, Jericho began returning to his 1999-2001 Y2J character as an anti-hero/tweener when he explained his actions by claiming all the other wrestlers in WWE were imitations of himself, referring to many main-eventers and naming CM Punk as the worst offender by calling himself the "Best in the World". Jericho was placed in an Elimination Chamber match for the WWE Championship and won a Six-Pack Challenge against the other competitors to be the final entrant into the Elimination Chamber match. At the Elimination Chamber event, Jericho eliminated Dolph Ziggler and Kofi Kingston but was kicked out of the Chamber by Punk, which gave him a head injury and removed him from the match without being eliminated. The following night on Raw, Jericho won a ten-man Battle Royal making him the number one contender for CM Punk's WWE Championship at Wrestlemania XXVIII. In a bid to psychologically unsettle Punk before their WrestleMania match, Jericho revealed that Punk's father was an alcoholic and Punk's sister was a drug addict which led Punk to his straight edge philosophy; Jericho also vowed to make Punk turn to alcohol by winning Punk's title from him. At WrestleMania, an additional stipulation was added that Punk would lose his WWE Championship if he was disqualified. During the match, Jericho's efforts to taunt Punk into disqualifying himself were unsuccessful as Punk managed to beat Jericho to retain the title. On the April 2 and 9 editions of Raw, Jericho continued his feud with Punk by attacking and dousing him with alcohol after his matches with Mark Henry. At Extreme Rules, Jericho failed again to capture the WWE Championship from Punk in a Chicago Street Fight.
On the May 7 episode of Raw SuperShow, Jericho pinned World Heavyweight Champion Sheamus during his tag team match with Alberto Del Rio against Sheamus and Randy Orton. After the match, Jericho, Orton, and Del Rio demanded a match for Sheamus' title at the Over the Limit, which they were granted; Sheamus pinned Jericho at the event to retain the title.
On May 24, at a WWE live event in Brazil, Jericho wrestled a match against CM Punk, during which Jericho crumpled up and kicked a Brazilian flag. Local police then intervened, threatening Jericho with arrest. Jericho issued an apology to the audience later on in the match, enabling the event to resume. The following day, WWE suspended Jericho indefinitely for denigrating the Brazilian flag.
On the June 25 episode of Raw Supershow Jericho made his return to Raw, interrupting John Cena, announcing himself as the third man in the WWE Championship Money in the Bank match alongside Cena and the Big Show, and then losing to Cena via disqualification due to interference from Show. At Money in the Bank, he was unsuccessful as the match was won by Cena.
The following night on Raw, Jericho confronted newly crowned Mr. Money in the Bank, Dolph Ziggler, however Ziggler would interrupt him and claim that he had lost his touch. This resulted in Jericho hitting Ziggler with a Codebreaker, thus turning face. The following week, on Raw 1000, Jericho teamed with Ziggler and Alberto Del Rio against Sheamus, Sin Cara, and Rey Mysterio; Jericho was pinned by Sheamus after Ziggler punched Jericho off the apron. Four days later on SmackDown, Jericho further cemented his face turn by attacking Ziggler whilst wearing Ziggler's signature shirt. Three days later on Raw, he solidified his turn by teaming up with Christian in a winning effort against Ziggler and The Miz. After the match, Ziggler hit Jericho with his Money in the Bank briefcase. On the August 6 episode of Raw, Jericho would cost Ziggler his match against Alex Riley after Jericho distracted on commentary. Four days later on Smackdown, Jericho hosted the Highlight Reel with Vickie Guerrero as guest, where he returned to his Y2J gimmick before being attacked by Ziggler. At SummerSlam, Jericho defeated Ziggler in a singles match by locking him in the Walls of Jericho. The following night on Raw, Ziggler defeated Jericho in a rematch; as a result, Ziggler retained his Money in the Bank contract and Jericho's WWE contract was terminated as per a the pre match stipulation put in place by Raw general manager, AJ Lee. After the match, Jericho attacked Ziggler with his own briefcase and hit a Codebreaker before leaving the arena. This was used to write him off so he could tour with Fozzy for the remainder of the year. Right after these events, Jericho's WWE profile was moved to the 'Alumni' section of their website.
On January 27, 2013, Jericho returned after a six-month hiatus entering the Royal Rumble match as the second entrant. Jericho lasted over 47 minutes before being eliminated by Dolph Ziggler. The following night on Raw, Jericho later revealed to Ziggler that due to a managerial change on Raw, he had been rehired by Vickie Guerrero, resuming his feud with Ziggler. Guerrero then placed the two in a "Strange Bedfellows" match against WWE Tag Team Champions Team Hell No (Daniel Bryan and Kane). The match ended with Ziggler being chokeslammed and pinned by Kane after Jericho framed him for pushing Kane. The following week on Raw, Jericho won a poll to face CM Punk in a Wrestlemania rematch, but was defeated. On the February 11 episode of Raw, Jericho defeated Daniel Bryan to qualify for a spot in the number one contender Elimination Chamber match for the World Heavyweight Championship. Six days later at the Elimination Chamber pay-per-view, Jericho was the fourth man eliminated from the match by Randy Orton. The following night on Raw, Jericho teamed with Ryback and Sheamus to face their rivals The Shield (Dean Ambrose, Roman Reigns, and Seth Rollins), but were defeated after Ambrose pinned Jericho for the win. On the March 11 episode of Raw, Jericho faced The Miz in a number one contenders match for Wade Barrett for his Intercontinental Championship, but the match was ruled a no contest after Barrett interfered and attacked both men. As a result, both men were entered into the title match the following week on Raw, where Barrett retained his title. Earlier in the episode, Jericho had a run-in with Fandango which led to Fandango costing him his match with Jack Swagger and attacking him four days later on SmackDown. On the next episode of Raw, Jericho attacked Fandango and then immediately defeated old rival Dolph Ziggler via submission. Afterwards, Jericho was attacked by both Ziggler's ally Big E. Langston and Fandango which started a feud between him and Fandango. On April 7 at Wrestlemania 29, Jericho was defeated by Fandango in a singles match. On April 13 episode of Smackdown at Boston, Chris Jericho was defeated by Dolph Ziggler. In the aftermath, both Ziggler and Langston hit their respective finishers on the fallen Jericho, before Fandango added his own leg drop off the top rope. Three days later on Raw, Jericho was again defeated by Ziggler after Fandango's theme song played and allowed Ziggler to capitalize on the distraction. Later that night, Jericho attacked Fandango following a match and proceeded to dance with Fandango's dancer. At Extreme Rules, Jericho defeated Fandango. On May 27th edition of Raw on the Highlight Reel, Jericho had Paul Heyman as a guest on his show. He questioned Heyman about the return of his client CM Punk . Jericho then challenged Punk at the next PPV Payback in which Heyman accepted on Punk's behalf. At the pay-per-view on June 16, Jericho was unsuccessful in his attempt to defeat the returning Punk. On June 24, episode of RAW, Jericho was booked in a singles match against Ryback at Money in the Bank pay-per-view by Vickie Guerrero after the pair had complained about being left off the PPV. Ryback would go on to win the match. The following night on Raw, Jericho was defeated in a match by Rob Van Dam. On the July 19 SmackDown, he lost to Curtis Axel in an Intercontinental Championship match. After the match, Ryback came down and gave him a shell-shocked. This would be Jericho's last match for this run as he announced he's taking another hiatus.
On the June 30th episode of Raw, Jericho returned to confront The Miz only to be attacked by The Wyatt Family. This set up a match between Jericho and Wyatt at Battleground, which Jericho won. Wyatt Faced Jericho again in Summerslam which Wyatt won after delivering his finishing move Sister Abigail on the barricade and pulling him to the ring and performing it again and pinned him. At Night Of Champions, Jericho would lose to Randy Orton after Orton performed an RKO in mid-air.
Jericho returned on the November 14 episode of SmackDown, hosting the Highlight Reel with The Authority as guests. The following month, Jericho was the Guest General Manager of the December 15 episode of Raw, where he hosted the Highlight Reel with Rusev and Lana as his guests and booking himself in a match against Paul Heyman. The match would never officially start after a returning Brock Lesnar would attack Jericho.
Jericho would face and defeat Luke Harper at both his first and second live event dates under the new contract on January 10 and January 11 in Montgomery, Alabama and Mobile, Alabama. In May, Jericho would be announced as the host of the sixth season of WWE Tough Enough. On the July 4 WWE Network special event, Jericho would defeat Neville by submission.
On September 20, 2015, at Night of Champions, Jericho was revealed as the mystery tag team partner of Roman Reigns and Dean Ambrose against the Wyatt Family, but after losing the match, would walk away from Reigns and Ambrose, bumping Ambrose in the process, hinting at a possible heel turn. Two weeks later Chris Jericho was defeated by Intercontinental Champion Kevin Owens at the WWE Network Special Live from Madison Square Garden.
Jericho made his return on the January 4, 2016 episode of Raw to confront The New Day, announcing that he would participate in the 2016 Royal Rumble match. In the Royal Rumble match, Jericho lasted over 50 minutes and scored one elimination before being eliminated by Dean Ambrose. The following night, on the January 25 edition of 'Raw', Jericho appeared in a backstage segment with AJ Styles and later lost in a singles match against him. After initial hesitation by Jericho, the pair shook hands to close out the segment. On the February 4 Smackdown, Jericho challenged Styles to a rematch the next week, asking if "he was good enough to beat him twice", which Styles accepted. On the February 8 episode of Raw, Styles interrupted a Highlight Reel (originally Miz TV) segment, coming to the aid of Jericho after he had been attacked from behind by The Miz. On the February 11 Smackdown, Jericho and Styles defeated The Social Outcasts, Adam Rose and Curtis Axel in an impromptu match; during which both men tried to one-up each other. Later in the main event, Jericho defeated Styles via a Codebreaker. On the February 15 episode of Raw, after Styles defeated The Miz, Styles challenged Jericho to a match at Fastlane, to which Jericho said that he will think about it and he will tell Styles what he will say on Smackdown. On Smackdown, Jericho would initially decline the challenge, but would later accept after Styles attacked him. At Fastlane, Styles defeated Jericho via the Calf Crusher.
The night after Fastlane, on the February 22 episode of Raw, Jericho and Styles would form a tag team (dubbed Y2AJ), defeating Social Outcasts members Heath Slater and Curtis Axel. On the February 25 episode of SmackDown, Styles, Jericho and Mark Henry defeated The New Day in a six-man tag team match, in which Styles got the submission victory for the team over Xavier Woods. The team would defeat the New Day once again on "RAW" where Jericho got the submission against Kofi Kingston. On the March 7 episode of Raw, Jericho and Styles faced The New Day for the WWE Tag Team Championship, but were defeated after Jericho was pinned by Big E. After the match, Styles helped Jericho up to his feet, but Jericho responded with three Codebreakers to Styles, before shoving their "Y2AJ" shirt into Styles' mouth, thus turning heel for the first time since 2012 and re-igniting their feud. On that weeks taping of SmackDown, Jericho went on to say he turned on AJ Styles because he was sick of the fans chanting for AJ and not him. Jericho went on to throw their Y2AJ shirt into a bin and light it on fire. On March 12 at the WWE Roadblock special, Jericho went on to defeat Jack Swagger via submission. Before this match, Jericho cemented his turn by berating the Canadian crowd. On the following nights AJ and Chris distracted each other in their matches. Styles said that he would show Jericho why they chant "AJ Styles", if Jericho accepts his challenge for a match at WrestleMania 32. Jericho initially declined the challenge backstage in an interview saying that "[Styles] didn't deserve it," but on the March 28 episode of Raw, Jericho accepted the match after AJ Styles caused him to lose a match to Zack Ryder. However at Wrestlemania 32, Styles was defeated by Jericho, giving Chris his first Wrestlemania win since 2010.
On the Raw after WrestleMania 32, Jericho was in a Fatal 4 Way match to be the #1 contender for Roman Reigns' WWE World Heavyweight Championship against the returning Cesaro (who replaced Sami Zayn), Kevin Owens, and rival AJ Styles. The match was won by Styles, who pinned Jericho. he next week on Raw, Jericho hosted an episode of The Highlight Reel, but the show was cancelled by Shane McMahon and replaced with Dean Ambrose's Ambrose Asylum, igniting a feud between the two. On May 1 at Payback, Jericho faced Ambrose in a losing effort. On the following episodes of Raw, Jericho destroyed Ambrose's potted plant from his "Ambrose Asylum" set, while Ambrose ripped apart Jericho's $15,000 light-up jacket. On the next week's Raw, Ambrose challenged him to a match at Extreme Rules in the first ever Asylum Match, where the ring is enclosed by a steel cage with asylum hospital weapons at the top of the cage, such as a straitjacket. Jericho ended the match in a losing effort, after being slammed back-first into a pile of thumbtacks. On the May 23 episode of Raw, Jericho would defeat Apollo Crews to qualify for the Money in the Bank ladder match at the Money in the Bank pay-per-view. At the event, Jericho was unsuccessful as the match was won by Dean Ambrose.
On July 19, at the 2016 WWE Draft, Jericho was drafted to Raw. He would go on to defeat Cesaro in a singles contest later that evening. At Battleground, Jericho hosted a Highlight Reel segment with the returning Randy Orton. The next night on RAW, Jericho competed in a Fatal Four Way match to determine the number one contender for the WWE Universal Championship at SummerSlam but was ultimately unsuccessful. Jericho would then enter a feud with Enzo Amore & Big Cass. On the August 1 episode of Raw, he teamed with Charlotte to defeat Women's Champion Sasha Banks and Enzo Amore in mixed tag team action. After the match, Cass would make the save as Chris Jericho attempted to continue the assault on Enzo. On the August 8 episode of Raw, Chris Jericho would reveal a new tag team partner in Kevin Owens. He would later go on to defeat Enzo Amore via disqualification later in the evening when Big Cass interfered. At SummerSlam, Jeri-KO defeated Enzo & Cass via pinfall after debuting a new finisher, the pop-up codebreaker on Enzo. On the August 22 episode of RAW, Jericho interfered in Kevin Owen's match against Neville, allowing him to win and qualify for the fatal four-way match to determine the new WWE Universal Champion on the August 29 episode of RAW. Owens later attempted to aid Chris Jericho in his qualifying match against Roman Reigns but was ultimately unsuccessful. On the September 12 Raw, Jericho hosted an episode of The Highlight Reel with Sami Zayn as his guest, who questioned his alliance with newly crowned Universal Champion Kevin Owens, resulting in Jericho defending Owens and attacking Zayn. At Clash of Champions, Jericho defeated Zayn, and later assisted Owens in his victory against Seth Rollins. On the October 10 episode of Raw, Jericho would lose to Seth Rollins in the main event. Had Jericho won, he would have been added to the Hell in a Cell match for the WWE Universal Championship at the pay-per-view. On the October 24 Raw, he lost a Triple Threat Match to Rollins when Rollins pinned both Jericho and Owens. At Hell in a Cell, Jericho aided Kevin Owens to victory against Seth Rollins after Owens would spray a fire extinguisher in the face of the official which in turn allowed Jericho entry into the Hell in a Cell structure. After the match, Jericho would hit Rollins with a codebreaker before his music played. The next night on Raw, Jericho faced Roman Reigns in the main event for the United States Title, but failed to win after Owens interfered for the disqualification. Jericho was later announced as co-captain of Team RAW for the Traditional 5-on-5 Survivor Series inter-promotional elimination tag team match against Team SmackDown Live, alongside Kevin Owens. On the November 7 episode of Raw, Jericho competed in a Fatal Five Way match against fellow Team RAW members Kevin Owens, Roman Reigns, Seth Rollins and Braun Strowman which was won by Owens after pinning Jericho unintentionally. At Survivor Series, Team RAW were unsuccessful in defeating Team SmackDown Live. The next night on Raw, after teasing a break-up earlier in the night during Jericho's Highlight Reel segment, Jericho would go on to aide Owens to a successful title defense during the main event of Raw against Seth Rollins. Despite being banned from ringside for the match, Jericho appeared in the crowd in a luchador mask and attacked Rollins. The next week on Raw, when Jericho was leaving the arena, he was attacked in the parking lot by Seth Rollins, and received a pedigree on top of a car. On the December 5 episode of Raw, Owens announced that Jericho will face Rollins at Roadblock: End of the Line, while later on that same night, Jericho failed to capture the United States Championship from Reigns after unwanted assistance from Owens. At Roadblock, Jericho was defeated by Rollins. Later on the night Jericho delivered a Code-Breaker to Owens on purpose to give him a disqualification win and another successful title defense this time against Reigns. On December 19th episode of Raw, it was announced that Owens will face Reigns in a rematch for the Universal Championship at Royal Rumble with Jericho suspended above the ring in a shark cage. On the first episode of Raw in 2017, Jericho announced that he would also take part in the 2017 Royal Rumble match.