A 67-year-old man presented with bloody stools. Colonoscopy showed a small submucosal tumor in the lower rectum. As the tumor was small, follow-up was chosen. Although he was instructed to undergo reexamination 1 year later, he did not comply. Four years later, he was reexamined by the previous doctor for disorders of defecation. He was admitted to our hospital for examination and treatment, as the tumor was growing. The mass measured 87×69 mm. The tumor was found on the dorsal side of the rectum with well-circumscribed, smooth margins. Trans-anal biopsy showed rectal GIST. The tumor seemed difficult to resect, and hence, imatinib mesylate(400mg/day)was administered as neoadjuvant chemotherapy for tumor reduction. After 4 months, the maximum tumor diameter was reduced by 60%, and arthroscopic surgery was performed by 2 teams. In the trans-anal arthroscopic operation, partial resection of the levator ani muscle was performed, and complete excision was achieved by securing the excision margin. The operation time was 341 min, and the hemorrhage volume was 422 mL. Postoperatively, a Grade 2 suture failure occurred at the anastomotic site, but no further complications were observed.