After being selected by the New York Mets with the 24th overall pick of the 1980 amateur draft, Gibbons had a very brief 18-game major league playing career as a catcher with the Mets in 1984 and 1986. In 1984 he was considered to be the Mets' top catching prospect but he batted only .220, with one home run and 2 RBIs (but 16 strikeouts) in 50 at-bats. Injuries also took a toll on him so he retired as a player in 1990. Gibbons served as the Mets' bullpen catcher during the 1986 postseason, in which the Mets won the World Series.
After Ricciardi fired manager Carlos Tosca in 2004, Gibbons was promoted to the manager position. The Blue Jays went 20-30 with Gibbons at the helm.
At the end of the 2004 regular season, Gibbons signed a one-year contract as the manager for the 2005 season. This contract was extended for three seasons just a week into the 2005 season. Gibbons went on to lead the Jays to an 80-82 record in his first full season as a big league manager.
Expectations were higher in 2006, after the Blue Jays acquired A. J. Burnett, Troy Glaus, Lyle Overbay, B. J. Ryan, and Bengie Molina. Toronto ended the season in second place in the American League East division with an 87-75 record, one game ahead of the Boston Red Sox. Although they finished 10 games out of first, it was the first time the Jays had finished higher than third since 1993, when they won their second of two consecutive World Series titles.
With the Blue Jays mired in a slump that put them five games below .500, Gibbons was fired on June 20, 2008. He was replaced by former Jays manager Cito Gaston. He finished with a record of 305 wins and 305 losses.
Kansas City Royals and San Antonio Missions (2009-2012)
On November 20, 2012, it was announced that Gibbons was re-hired as manager of the Toronto Blue Jays on a two-year rolling contract. Gibbons was named to the 2013 American League All-Star coaching staff by Detroit Tigers manager Jim Leyland. The Blue Jays finished the 2013 season with a 74-88 record, putting them last in the AL East.
The Blue Jays were six games up in the AL East title race on June 6, 2014, but posted a 45-54 record from that point on, including a 9-17 record in August. They would finish the season with a record of 83-79, good enough for third place in the AL East, and five games back of a wild card spot.
On June 22, 2015, the Blue Jays defeated the Tampa Bay Rays 8-5 for Gibbons' 500th managerial win. On August 2, Gibbons was ejected for the third time in the 2015 season, for arguing with umpire Jim Wolf. Gibbons returned to the field later in the game during a bench-clearing incident, and was subsequently suspended for one game. On September 25, Gibbons and the Blue Jays ended the team's 22-year playoff drought by clinching a playoff berth. Five days later, the Blue Jays defeated the Baltimore Orioles 15-2, and clinched the American League East. On October 14, 2015 the Blue Jays defeated the Texas Rangers to win the American League Division Series after losing the first two games of the series. The Blue Jays moved on to play in their first American League Championship Series since 1993. They were defeated by the eventual World Series champions, the Kansas City Royals, in six games.
On April 5, 2016, after a 3-2 loss to the Tampa Bay Rays ended on a questionable slide by José Bautista which was ruled as a double play, Gibbons stated, "Maybe we'll come out and wear dresses tomorrow. Maybe that's what everybody's looking for." A day later, after he received criticism for his initial comment, he said that "the world needs to lighten up a little bit". On May 17, Gibbons was suspended three games by Major League Baseball for his role in a benches-clearing incident between the Blue Jays and Texas Rangers on May 15 involving Rangers infielder Rougned Odor and Blue Jays outfielder José Bautista. On September 11, Gibbons was ejected for the eighth time in the 2016 season, tying the team's single-season record set by Bobby Cox; he led the major leagues in 2016. In 2016 he was successful on a lower percentage of replay challenges than any other MLB manager with 10 or more challenges, at 38.8%. The Blue Jays made the playoffs for the second consecutive season, and defeated Baltimore in the Wild Card Game to advance. In the Division Series, the Blue Jays swept the Texas Rangers in three games. Toronto was eliminated by the Cleveland Indians in the Championship Series, four games to one.
On April 1, 2017, Gibbons signed a two-year extension with the Blue Jays, that also included an option for the 2020 season. In 2017 he was again successful on a lower percentage of replay challenges than any other MLB manager with 10 or more challenges, at 26.7%.
On September 26, 2018 it was confirmed by the Blue Jays that Gibbons would not return for the 2019 season. Toronto mayor John Tory proclaimed the 26th as "John Gibbons Day" in Toronto, noting Gibbons' "tremendous contributions to the Toronto Blue Jays franchise." His final game was a 9-4 loss to the Tampa Bay Rays. The Blue Jays finished the 2018 season with a 73-89 record. In 2018 he was ejected seven times, more than any other manager in the major leagues. During his second stint as Blue Jays manager, he finished with a record of 488 wins and 484 losses. Overall, Gibbons has a 793-789 record from both stints as Blue Jays manager.
On May 28, 2005, Gibbons chastised former Toronto starter Dave Bush in the dugout after the right-hander showed his displeasure on the mound about being removed from a game. The next day Bush was sent to the minor leagues  and after the season, he was traded to the Milwaukee Brewers.
Gibbons was again involved in controversy in July 2006, after his feud with Shea Hillenbrand came to a head. After the Blue Jays infielder and designated hitter wrote negative comments about the team on a display board in the Blue Jays clubhouse, Gibbons confronted him in a closed team meeting and challenged him to a fight. Hillenbrand declined to fight. Hillenbrand was upset about his lack of playing time and that no one in the Blue Jays front office had made an attempt to congratulate him on recently adopting a child. Three days later the Blue Jays traded Hillenbrand, who was hitting .301 at the time, to the San Francisco Giants. In 2012, after Gibbons was re-hired as the Blue Jays manager, Hillenbrand endorsed the hiring and acknowledged that he, not Gibbons, was at fault for the controversy, saying "I think he handled the situation that we had very professionally and I didn't handle it professionally at all. I think John's going to be a great addition to that ball club and he's a great guy."
On August 21, 2006, Gibbons walked to the mound in the third inning to remove pitcher Ted Lilly from Toronto's game against the Oakland Athletics. Visibly frustrated at his own performance (having given up 7 runs in that inning to erase an 8-0 lead), Lilly initially refused to surrender the ball to Gibbons. Words were exchanged and Lilly left the mound and headed for the clubhouse. When Gibbons returned to the dugout, he followed Lilly into the clubhouse tunnel where, according to eyewitnesses, he confronted his pitcher regarding his insubordination. Cameramen saw Gibbons push Lilly first. "Gibbons just went at him," photographer Aaron Harris said. The two exchanged shoves, and a number of players and Blue Jays staff rushed in from the dugout to break it up. During MLB's 2014 winter meetings, Lilly was working as a front-office member of the Chicago Cubs. Signalling that he harbored no hard feelings, Gibbons stuck his head into a Chicago hotel suite filled with media and laughingly called Lilly out.
At the beginning of the 2008 season, Gibbons benched future Hall-of-Famer Frank Thomas, who had a batting average of .167 after the first 20 games of the season. Thomas, typically a slow starter, was livid over his lack of playing time. He claimed that the Blue Jays were giving him less playing time to prevent him from getting 364 at-bats in the season, which was the required amount for his $10 million 2009 option to become guaranteed. The Blue Jays responded the next day on April 20, 2008, by releasing Thomas. Blue Jays general manager J.P. Ricciardi met with Thomas and they agreed that the best thing for the team and for Thomas would be to let him go. Thomas returned to the Oakland Athletics and hit well despite some struggle with injury. It was his last season in the Major Leagues.
After striking out for the second time in three innings in a game against the New York Yankees on August 16, 2016, Blue Jays third baseman and reigning American League MVP Josh Donaldson returned to the dugout and angrily threw his bat against a bat-rack very close to where Gibbons was standing. Gibbons quickly confronted Donaldson, and the pair got into a short argument in an incident that was caught on camera. Blue Jays' players Troy Tulowitzki and Josh Thole stepped in to restrain Donaldson. The incident, while creating "fabulous talk-show fodder", was ultimately quickly forgotten. Said Gibbons after the game, "I told him after the first at-bat, get a new bat, that one ain't working. He took the same one up the second time. That didn't work. He chose to break it. So I went down and told him, you should have listened to me. That was basically it." Donaldson downplayed the altercation as well, saying that Gibbons simply wanted a better smell of a new cologne Donaldson was wearing.