We performed targeted molecular therapy in a patient with a non-resectable pelvic gastrointestinal stromal tumor (GIST). Imatinib mesylate was administered at 400-600 mg/day for 6 months, and the tumor became resectable. The patient was a 58-year-old female who visited a gynecologic hospital with the chief complaint of a swollen feeling in the lower abdomen. A pelvic tumor was found by imaging, and the patient was referred to our hospital. Laparotomy was performed, but it was found that the tumor arose from the intestinal serous membrane, rather than from the uterus, and complete excision was difficult. A portion of the tumor tissue was excised, and the abdomen was closed. GIST was diagnosed on postoperative pathological examination, and the tissue was positive for c-kit protein on immunostaining. The tumor had markedly shrunk after oral administration of imatinib mesylate for 6 months, and excision by laparotomy became possible.