Gee's return to throwing and other baseball activity is undetermined, according to a release by the Mets.
Gee underwent a procedure to clear a blood clot earlier this past week; Friday's surgery was to prevent future clotting.
Gee had been scheduled to start Friday's series opener against the Braves. Instead, right-hander Chris Young got the start. Young has made six starts this season and has a 3.41 ERA in 37 innings.
Young, who has struggled with injuries throughout his nine-year Major League career and who missed the first two months of this season, will be asked to become a regular in the rotation.
Manager Terry Collins said that the prospect of Young pitching every fifth day doesn't concern him.
"He's smart enough to know that he's got to do it right," Collins said, "And he will, because he plans on playing longer than just this summer. So he wants to make sure he doesn't do anything to hinder that."
Gee's injury also opens a spot in the rotation. For now the Mets will move right-hander Miguel Batista out of the bullpen and into that spot, but promoting top prospect Matt Harvey is not out of the question.
Collins wouldn't even rule out using Harvey the next time the Mets need a fifth starter.
"We're in the hunt," Collins said. "This isn't a tryout camp. So if the people who see him say he's ready, bring him up. I'm all for it."
Harvey is 7-4 with a 3.39 ERA and 102 strikeouts in 98 1/3 innings at Triple-A Buffalo. He threw two shutout innings and struck out two in the Triple-A All-Star Game on Wednesday night.
Teddy Cahill is an associate reporter for MLB.com. This story was not subject to the approval of Major League Baseball or its clubs.