2008-2012
McGowan had compiled a 6–7 record with an ERA of 4.37 and 85 strikeouts prior to the 2008 All-Star break. But on July 8, he was forced to leave the game early with pain in his shoulder. On July 10, he was put on the 15 day disabled list. Then on July 26, it was announced that McGowan would undergo season-ending surgery to repair fraying of the labrum in his shoulder. He was expected to return during the 2009 season, but his recovery was slower than initially anticipated. McGowan began throwing from level ground in early May 2009. However, further injury befell him and on July 9, 2009, McGowan had knee surgery to repair articular cartilage damage, requiring six weeks of recovery before continuing his rehabilition programme.
McGowan was expected to pitch sometime in June 2010, but he experienced shoulder pain during early June and it was found that he has a torn rotator cuff and had season ending surgery, he was expected to have to wait 4–6 months before he could resume throwing. It was hoped that McGowan can recover and be ready for the 2011 season, of the second surgery GM Alex Anthopoulos said that "We're optimistic that he'll be able to come back and we'll continue to work with him once he starts throwing."
On August 2, 2011, Manager John Farrell said he expected to add McGowan to the Jays rotation sometime in September. He was expected to join the Double-A New Hampshire Fisher Cats after one more start with the Advanced-A Dunedin Blue Jays.
On September 5, 2011, McGowan was activated from the 60-day disabled list. The following day, McGowan made his first appearance in over 3 years, against the Boston Red Sox. McGowan pitched 4 innings, and gave up 3 earned runs while striking out 5 and walking 3.
On March 26, 2012, McGowan signed a 2 year contract extension for $3 million with a club option for 2015 worth $4 million.
On August 7, 2012, it was announced that McGowan would undergo arthroscopic shoulder surgery on August 9, to evaluate the recovery of his right shoulder.
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