General manager Terry Ryan said before Tuesday's game against the White Sox that he expects the 30-year-old Hughes to be ready for the start of spring training.
Hughes suffered a fracture of the femur above his knee when he was hit by a line drive by Miami's J.T. Realmuto on June 9 and was expected to miss at least two months with that injury.
But Ryan said Hughes was also experiencing right shoulder pain. He was diagnosed with thoracic outlet syndrome. Surgery on July 6 will require removing a rib.
Hughes had struggled and lost velocity amid pain and fatigue in his shoulder and was demoted to the bullpen before he was hurt. He was 1-7 with a 5.95 ERA this season.
Hughes has three years and $39.6 million left on his contract after this season.