Toronto's oft-injured righty was expected to open the year as the club's No. 5 starter, but a right foot injury forced him to be shut down late in camp.
McGowan had to stop throwing for almost a month, meaning he will be out for at least the next six weeks as he tries to build up arm strength.
"In some ways, he's starting Spring Training again," Blue Jays manager John Farrell said.
McGowan's work will start with throwing off flat ground from 60 feet every two days. He will eventually be extended to 90 feet and then 120, before getting back onto the mound.
A decision on who will be McGowan's replacement is expected later in the week, but whoever it ends up being, Toronto hopes to settle on one person.
"You don't want to have a revolving door and you're hoping you can have someone who can stay," Blue Jays general manager Alex Anthopoulos said. "That's where you're relying on your staff. [Triple-A righty Jesse] Chavez really made a good push with his last start, he pitched great, and the staff was very excited about him. I'm not saying that to lead the witness or to drop the hint, but it's the truth. He wasn't as strong a candidate until that last start, he really looked good."