Gastrointestinal stromal tumors (GISTs) of the rectum are rare, and their clinical manifestations are variable. We report the case of a 23-year-old woman who was referred complaining of dyspareunia during coitus. We performed digital vaginal and rectal investigations, ultrasound, colonoscopy, and computed tomography. These examinations confirmed the presence of a lesion measuring about 6 x 5 x 5 cm in size attached to the posterolateral left rectum wall. We performed a circumanal excision, then arrived at the mass between the muscles of the pelvic floor. Pathological studies indicated that the tumor was a high-grade GIST, and was clear at the surgical margins. On follow-up, a GIST was found at the gastric fundus via an endoscopic biopsy. Imatinib treatment was initiated because the patient refused a second operation. The gastric lesion disappeared 6 months after imatinib treatment. Dyspareunia disappeared 1 month after operation.