While the operation is being performed, McGowan will also have his right rotator cuff examined to determine if there is further damage in that area.
The tear in McGowan's rotator cuff was what initially forced the 26-year-old starter to the disabled list on June 9, a day after he lasted just 66 pitches in a start against the Orioles.
Earlier in the month, the Jays compared McGowan's latest MRI results to a similar exam performed a year ago. The team determined that there was no further damage to the arm. Thursday's surgery will look to confirm this.
Jays general manager J.P. Ricciardi indicated on Saturday that if McGowan's rotator cuff does not require attention, then it is possible that he could return to the team by next year's Spring Training.
"It's unfortunate for him, obviously, but the good news is we'll have him back next year," Ricciardi said. "That's pretty encouraging.
"Right now, from what they've told us, if all that's in there is the fraying [and] nothing more, he should be OK for next year," Ricciardi added.
The GM did not know when McGowan will be allowed to resume a throwing schedule. For now, the right-hander will travel to Cincinnati to have the surgery performed by Dr. Timothy Kremchek.
In 19 starts for the Blue Jays this season, McGowan is 6-7 with a 4.37 ERA and 85 strikeouts across 111 1/3 innings.
The loss for McGowan is disappointing for the Jays, whose starting rotation has also taken a hit with Jesse Litsch's recent struggles and subsequent demotion to Triple-A Syracuse.
"We've been pretty resilient the last few years -- it's just part of the game," said Ricciardi. "We'll just have to get through it. Guys like [David Purcey will have to] come in here and step it up and help us out."
Jays manager Cito Gaston has already indicated that with McGowan lost for the season, the 26-year-old Purcey will be in the rotation for the foreseeable future. The left-handed starter, who spent most of the season in Syracuse, earned his first Major League victory on Saturday.
"It's always nice to have a left-handed starter in there too," Gaston said of Purcey. "If he can continue to go out and pitch like he did [on Saturday] -- just give us a chance to win ballgames, and that's what he did."
David Singh is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.