McGowan was drafted by the Toronto Blue Jays out of Long County High School in Ludowici, Georgia in the first round (33rd overall) of the draft on June 4, 2000, and signed with the Blue Jays on June 20, 2000. He began his career with the Medicine Hat Blue Jays where he was 0–3 with a 6.48 ERA in eight starts. In 2002 with the Charleston AlleyCats of the South Atlantic League he was 11–10 with a 4.19 ERA in 28 starts and led the league and the organization with 163 strikeouts. On May 21, 2003, he pitched a complete game shutout for the Dunedin Blue Jays of the Florida State League. His 2004 season was cut short when he underwent Tommy John surgery on his elbow on May 13.

On July 30, 2005, McGowan was called-up and made his debut that same day against the Texas Rangers. He received a no decision, having pitched 5 innings and allowing 1 run, and struck out six batters, the most by a Toronto starter in a Major League debut at the time.

McGowan bounced between the bullpen and the starting rotation during his first 2 seasons with the Blue Jays. He struggled in his rookie season following his impressive Major League debut, posting a 6.35 ERA in 13 games including 7 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.

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