He has previously played in Major League Baseball (MLB) for the St. Louis Cardinals, Minnesota Twins, New York Yankees, Texas Rangers, Chicago White Sox, and Los Angeles Dodgers.

Playing college baseball for the Ole Miss Rebels, Lynn set the school's single-season (146) and career (332) pitching strikeout records.

In 2009, he was named the Cardinals organizational Pitcher of the Year after playing in three levels and totaling a 2.85 earned run average and 124 strikeouts in 148+2⁄3 innings pitched.

He made his MLB debut on June 2, 2011, was a member of the Cardinals' World Series championship team that year, and a National League All-Star in 2012.

[2] He attended Brownsburg High School, where he played on the baseball team, with teammate Drew Storen, a fellow future major league pitcher.

As a pitcher, he posted a 1.26 earned run average (ERA) and 160 strikeouts (SO) in 100 innings pitched (IP), a 10–3 win–loss record, and three saves.

When Lynn played at the Area Code Games, Nike named him an All-Star, and he was teammates with fellow future Ole Miss Rebels baseball signees Evan Button and Scott Van Slyke.

In 2009, Lynn was named the Cardinals' organizational Pitcher of the Year after jumping three levels in his first full professional season.

[4] On September 10, 2010, Lynn broke the Redbirds' single-game franchise strikeout record, with 16 against the Oklahoma City RedHawks in a playoff game.

[4] On October 10, Lynn was awarded the win after throwing exactly one pitch in Game 2 of the National League Championship Series (NLCS) against the Milwaukee Brewers.

[7] In the World Series, Lynn gave up back-to-back home runs in the top of the seventh to Adrián Beltré and Nelson Cruz.

On the recommendation of the team chef Simon Lusky, Lynn decreased the amount of refined carbohydrates and fats in his diet.

[13] In a Spring Training game on March 14, Lynn struck out 10 Atlanta Braves in four innings, including the final eight hitters he faced.

Lynn, who had entered the game with a 6.55 ERA for the season, won his third decision behind 11 strikeouts and just three hits allowed as St. Louis prevailed 4–0.

[15] Against the Washington Nationals on April 19, he stroked his first career extra base hit — an RBI double — while picking up the decision for the win in a 4–3 victory.

[19] Baffling the Colorado Rockies on the corners of the strike zone on June 23, Lynn pitched another eight shutout innings in an 8–0 victory at Coors Field while allowing just three hits.

[30] Through that point in his major league career, he allowed a .248 batting average against,[31] and was the Cardinals all-time franchise leader with 8.7 K/9 among all players with at least 500 innings pitched for the club.

[11] On November 10, 2015, the Cardinals announced that Lynn would miss the 2016 season after undergoing Tommy John surgery (TJS).

On July 30, 2018, the Twins traded Lynn and cash considerations to the New York Yankees in exchange for Tyler Austin and Luis Rijo.

On December 7, 2020, Lynn was traded to the Chicago White Sox in exchange for pitcher Dane Dunning and prospect Avery Weems.

On July 17, 2021, Lynn agreed to a two-year, $38 million contract extension with Chicago that includes a club option.

Lynn went 5 innings, giving up 4 hits, 4 runs, and 2 walks while striking out 7 batters as the White Sox beat the Yankees 9-8.

Lynn started out the 2022 season on the Injured List after suffering a meniscus tear during spring training.

In that game after the 2nd inning, Lynn got into an argument in the dugout with White Sox third base coach Joe McEwing.

In the game, Lynn went 4.1 innings giving up 10 hits and 3 earned runs while striking out 4 batters as the White Sox won 9–5.

[47] On July 28, 2023, Lynn and Joe Kelly were traded to the Los Angeles Dodgers in exchange for Trayce Thompson, Nick Nastrini, and Jordan Leasure.

Overall, combined with both teams he played for in 2023, Lynn made 32 total starts with a 13–11 record, a 5.73 ERA, and an MLB-leading 44 home runs allowed.

He obtained team strength and conditioning coach Pete Prinzi's help in formulating an offseason training regimen to address his lapses and stimulate weight loss.

The Cardinals also sent team chef Lusky to spend a week with Lynn and his wife Lauren in their home, where he showed them better methods to select and prepare healthy food.

[10] In 2014, Lynn acknowledged how not handling his emotions during difficult innings affected his ability to limit damage from the opposition and finish off hitters with runners on base.