Vaginal cysts are common lesions that include Gartner cysts, which develop from the wolffian duct remnants in the vaginal wall. Malignant transformation of Gartner cysts is exceedingly rare. Our case was diagnosed upon evaluation of vaginal bleeding in a 67-year-old woman. Histologic examination showed a clear cell carcinoma. Treatment consisted of surgical excision and radiation therapy. Treatment quality, stage, and pelvic node status are the main prognostic factors. Regular long-term follow-up is crucial.