A ganglion cyst is a benign cystic lesion that can occur intraosseously. It is commonly a multiloculated lesion that consists of fibrous tissue with mucoid change and is usually located in the subchondral bone adjacent to the joint. Here, we present a rare case of a 33-year-old woman who presented to our orthopedic clinic with a five-year history of shoulder pain that gradually worsened. The pain was worst after any activity involving the right shoulder, and it also occurred at night and disturbed her sleep. Physical examination showed that the patient had limitations on the extreme range of movement. MRI revealed a subchondral bone cyst at the glenoid fossa. The ganglion cyst was subsequently curetted and packed with a bone graft from the iliac bone. Postoperatively, the pain resolved and the patient's range of movement improved. At the six-month follow-up, new bone formation over the void area caused by the cyst was observed on MRI.