A 60-year-old man presented to our hospital with melena. A submucosal tumor (24 mm) was found via magnetic resonance imaging between the prostate and the rectum (Rb). A gastrointestinal stromal tumor (GIST) that displaced the prostate ventrally was diagnosed via histopathology. Preoperative imatinib treatment was initiated to reduce the tumor size and prevent extensive surgery. Approximately 33% of the tumor was reduced using chemotherapy. First, laparoscopic rectal dissection and mobilization were performed reaching the pelvic floor. Then, we performed perineal partial rectal resection. There has been no recurrence.