The surgery is being performed by Braves orthopedic surgeon Dr. Xavier Duralde.
McCann dealt with soreness in his shoulder and tendinitis in his right knee this season. The shoulder problem didn't affect his throwing but contributed to his career-low .230 batting average this season.
McCann, a career .279 hitter, had 20 homers and 67 RBIs. He did not start in the Braves' wild-card loss to the St. Louis Cardinals.
The Braves will not know a recovery period for McCann until after Tuesday's surgery.
The team has until three days after the World Series to pick up their $12 million option for McCann in 2013.