He played in Major League Baseball (MLB) for the Toronto Blue Jays, Philadelphia Phillies, and Miami Marlins.

He received a no decision, having pitched five innings and allowing one run, and struck out six batters, the most by a Toronto starter in a Major League debut at the time.

He struggled in his rookie season following his impressive Major League debut, posting a 6.35 ERA in 13 games, including seven starts.

At the beginning of the 2006 season, he was recalled from the Syracuse SkyChiefs to take the place of the struggling reliever Jason Frasor.

In his second stint with the team McGowan struggled once again and was optioned back to Triple-A Syracuse on May 11 to work as a starter.

[7] He would redeem himself in his next start on June 24, 2007, as he had a no-hitter in the first eight innings against the Colorado Rockies at Rogers Centre, allowing only an 0–1 single to the first batter he faced in the ninth, designated hitter Jeff Baker, making him just the fifth pitcher in franchise history to carry a no-hitter into the ninth inning.

[8] On September 7, 2007, McGowan recorded a career high 12 strikeouts against the Tampa Bay Devil Rays, while giving up just two runs in eight innings of work.

Of his 27 games, 18 of them were quality starts, and he ranked second on the team with 169.2 innings pitched and 144 strikeouts to solidify his place as the number three starter in Toronto's rotation behind ace Roy Halladay and A. J. Burnett, where he began the 2008 campaign.

[10] Because of diabetes, McGowan started wearing prescription lenses to improve his vision in low-light conditions.

[13] Then on July 26, it was announced that McGowan would undergo season-ending surgery to repair fraying of the labrum in his shoulder.

However, further injury befell him and on July 9, 2009, McGowan had knee surgery to repair articular cartilage damage,[15] requiring six weeks of recovery before continuing his rehabilitation programme.

He was expected to join the Double-A New Hampshire Fisher Cats after one more start with the Advanced-A Dunedin Blue Jays.

[22] McGowan took part in a weighted ball training program to increase his velocity and shoulder strength during his recovery.

[28] McGowan was activated from the disabled list on September 1 when the rosters expanded, and announced his intention to compete for a job in the starting rotation in 2014.

[30] In a game against the Baltimore Orioles on April 11, 2014, McGowan earned his first win at any level, majors or minors, since June 22, 2008—a span of nearly six years.

[38] On August 3 with the Lehigh Valley IronPigs, McGowan allowed Mike Hessman's record-setting 433rd career Minor League home run.

On February 9, 2018, McGowan signed a minor league contract with the Tampa Bay Rays that included an invitation to spring training.

In June 2020, McGowan was hired by St. John Paul II Catholic High School in Tallahassee to coach their baseball team.