Stewart was originally selected by Cincinnati in the third round of the 2008 First-Year Player Draft before being traded to Toronto on July 31, 2009. He entered the 2010 season ranked as Toronto's No. 1 prospect according to Baseball America and went on to finish eighth in the Eastern League with a 3.63 ERA that season. In 2011, Stewart entered the season ranked as Toronto's fifth-best prospect, along with having the "Best Fastball" in the organization according to Baseball America.
The 26-year-old Stewart began the season as a member of the Chicago White Sox before being traded to Boston on June 24 along with infielder/outfielder Brent Lillibridge in exchange for infielder Kevin Youkilis. Stewart then went 3-5 with a 3.94 ERA (59.1ip/26er) in 11 starts with Triple- A Pawtucket before making two starts with the Red Sox on August 29 and September 30.