Goldberg signed a one year contract with World Wrestling Entertainment (WWE) in March 2003, debuting in WWE on the March 31 edition of Raw, the night after WrestleMania XIX. Immediately, he began a feud with The Rock by spearing him. Their rivalry intensified when The Rock held a segment entitled The Rock Concert, where he taunted Goldberg along with Gillberg. He defeated The Rock in his debut match at Backlash. The match was won by Goldberg following three spears and a Jackhammer. Goldberg went undefeated over the subsequent half-year, defeating 3-Minute Warning in his first match on Raw. Goldberg defeated Christian on the following edition of Raw in a steel cage match.
Goldberg next feuded with Chris Jericho. During Jericho's first edition 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 interrogatees 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 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.
Goldberg entered a rivalry with Triple H, challenging him for the World Heavyweight Championship at SummerSlam in the second Elimination Chamber match in WWE; after squashing and eliminating Randy Orton, Shawn Michaels, and Jericho, he was pinned by Triple H after Ric Flair threw a sledgehammer inside the Chamber. Triple H proceeded to attack Goldberg with the sledgehammer and as a result, Triple H retained the title. Goldberg continued his feud with Triple H and finally defeated him for the World Heavyweight Championship at Unforgiven, after agreeing to put his career on the line. The next night on Raw, Goldberg successfully retained the championship against Chris Jericho. A week later, Triple H issued a $100,000 bounty to anybody who could take Goldberg out of the game. Steven Richards, Mark Henry, La Résistance and Tommy Dreamer all attempted to collect the bounty but were unsuccessful. On October 20, Batista collected the bounty after he interfered in Goldberg's title defense against Shawn Michaels on Raw and attacked Goldberg, placing a folding chair around Goldberg's ankle and jumping off the middle rope onto the chair, shattering his ankle. Furious, Goldberg demanded a match against Batista. Triple H, however, got involved in the match between Goldberg and Batista trying to cripple Goldberg, but Goldberg fought back and speared Triple H before attacking Batista with a sledgehammer. At Survivor Series, Goldberg retained his championship against Triple H despite interference from Evolution.
On November 17, Goldberg faced Triple H, Randy Orton, and Batista in a Handicap match on Raw but was pinned following an RKO, a Batista Bomb and finally a Pedigree. After the match, Kane unexpectedly came out to seemingly assist Goldberg after Evolution continued their assault on him following the match. After scaring off Evolution however, he turned on Goldberg and chokeslammed him. The following week, Kane attacked Goldberg again while he was defending his championship against Triple H in a rematch from Survivor Series and later that night, expressed his desire to face Goldberg for the title. Raw General Manager Eric Bischoff announced that Goldberg would be defending his championship against both Kane and Triple H in a triple threat match at Armageddon. Goldberg teamed with Shawn Michaels and Rob Van Dam to face and defeat Kane, Batista, and Orton in a six-man tag team match. On December 8 on Raw, Goldberg faced Kane in a Lumberjack match which ended in a disqualification when Evolution and Mark Henry entered the ring and assaulted Goldberg. At Armageddon, Goldberg ultimately lost the title when Triple H pinned him after interference from Evolution and a chokeslam from Kane.
During the Royal Rumble in 2004, Goldberg crossed paths with then-WWE Champion Brock Lesnar when the latter interrupted Goldberg during a backstage interview. While Goldberg was in the midst of dominating the Royal Rumble, Brock Lesnar interfered in the match and hit Goldberg with the F-5. With his attention turned toward Lesnar, Kurt Angle eliminated a distracted Goldberg from behind. Goldberg vowed revenge on Lesnar and after defeating Mark Henry and Jonathan Coachman in a No DQ match, he declared Brock Lesnar his next victim. On February 2, Goldberg was given a front row ticket to No Way Out by Steve Austin. Smackdown! General Manager Paul Heyman appeared on Raw and, along with Vince McMahon attempted to get Goldberg to back off in his vendetta against Brock Lesnar which resulted in Goldberg spearing Heyman and accidentally spearing Austin when he was aiming for McMahon. Goldberg attended No Way Out as a fan, confronting Lesnar at the event and, after several insults by Brock Lesnar, entered the ring and executed a Jackhammer on him. Goldberg was then detained and escorted out of the arena by security guards. During the main event between Brock Lesnar and Eddie Guerrero, Goldberg reemerged from the crowd and cost Brock Lesnar the WWE Championship. This led to a match between the two being scheduled for WrestleMania XX with Austin serving as special guest referee. Fans knew this would be the final WWE match for both Goldberg and Brock Lesnar and thus gave largely negative reactions through the performance. After Goldberg defeated Brock Lesnar, both men received a Stone Cold Stunner from Austin.
On the May 31 episode of Raw, Goldberg was announced as the pre-order bonus for the WWE 2K17 video game. On the October 10, 2016 episode of Raw, it was announced that Goldberg would make his return to WWE on the October 17 episode of Raw to answer Paul Heyman's challenge to wrestle Brock Lesnar in a rematch from WrestleMania XX. On the October 11 episode of Talking Smack, Renee Young indicated that Goldberg had signed with the Raw brand, asking Smackdown Live General Manager Daniel Bryan, "What do you think about Raw recently signing Bill Goldberg?". The following week on Raw, Goldberg returned to WWE after 12 years, accepting Heyman's challenge. The following day, their match was scheduled at Survivor Series. On the October 31 episode of Raw, Goldberg returned to address Lesnar's comments from the previous week, only to be interrupted by Heyman, who teased that Lesnar was there, but Rusev came out instead. Goldberg hit a Jackhammer on Rusev, followed by a spear to Heyman, who was rushed to hospital with (kayfabe) broken ribs. On the final Raw before Survivor Series, Goldberg and Lesnar came face to face for the first time in twelve years, resulting in a brawl with security after Heyman insulted Goldberg's family. On November 20 at Survivor Series, Goldberg defeated Lesnar, surprising him with a spear after shoving him to the mat, before hitting another spear and finally a Jackhammer to win the match in just 1 minute and 26 seconds. Along with John Cena, he became only the second man to have defeated Lesnar on two separate pay-per view events. The next night on Raw, Goldberg thanked the fans and his family before saying he has one more title run left in him while also declaring himself as the first participant in the 2017 Royal Rumble match. The following week, Paul Heyman addressed the Survivor Series match, stating that they underestimated Goldberg, and that the match was a humiliation and embarrassment for him and Lesnar. He then stated that Lesnar would also be in the Royal Rumble as he has something to prove. Goldberg returned on the January 2, 2017 episode of Raw confronting Chris Jericho, who had just announced his participation in the Royal Rumble match, and WWE Universal Champion Kevin Owens, addressing that Jericho would be "first" in the Royal Rumble match and that he would challenge for the championship at Wrestlemania 33. Paul Heyman then came out to address what Brock Lesnar would do to everyone in the Royal Rumble match. United States Champion Roman Reigns then came out and stared down Goldberg. Braun Strowman then came out and announced his participation in the match. Goldberg and Reigns then hit simultaneous spears on Strowman.