McGowan experienced soreness in his right shoulder while rehabbing in Florida from a minor foot ailment. He was examined by renowned surgeon Dr. James Andrews on Wednesday, and while structural damage was ruled out, McGowan will be shut down for the next two weeks because of inflammation.
"Disappointing on a number of levels," manager John Farrell said. "First and foremost, you think about his path that he's come through. We've all talked about the resiliency, but the fact is we were banking on him to be a part of this rotation.
"We fully expect him at some point to be available, but it's a blow to our overall starting depth."
McGowan was slated to open the year as the Blue Jays' No. 5 starter, but was shut down late in camp after being diagnosed with plantar fasciitis in his right foot. The injury was only expected to keep McGowan out until early May, but the rehab did not go according to plan.
The 30-year-old had his throwing program delayed on multiple occasions, and when he was finally able to pick up a baseball, the pain quickly followed. McGowan was throwing off flat ground from short distances and when the club began to lengthen him out, the injury was revealed.
"When he was getting 100-120 feet, he was still in that early phase, he never got to really any flat ground or certainly not to the mound yet," Farrell said of McGowan, who signed a two-year contract extension in the spring.
"We felt like ... particularly in his case, that he might feel some discomfort in there or some tightness, not too much discomfort, but it persisted and he never seemed to get some freeness to it, and we made precautionary measures to take him in for an MRI and that's what it revealed."
McGowan's path of return to the big leagues has been filled with adversity. He returned in September following a three-year absence because of two major shoulder surgeries and one knee surgery and appeared to finally be turning a corner late in the year.
The native of Savannah, Ga., threw 21 innings for the Blue Jays and arrived in camp fully healthy for the first time in recent memory. Within a month, that had changed and while Toronto remains optimistic that McGowan will be back this season, there is no timetable for his return.