A 58-year-old Japanese man underwent colonoscopy. We identified a protruding submucosal tumor covered with normal mucosa to the level of the rectal ampullary lesion. The patient underwent convex endoscopic ultrasonography (EUS) and endoscopic ultrasonography-guided fine needle aspiration (EUS-FNA). EUS showed a hypoechoic mass with homogeneous internal echoes and regular margins. The lesion was contiguous with the fourth layer of the rectal wall. The histological specimen from EUS-FNA identified spindle cells. The immunohistochemical profile of the spindle cell tumor was as follows: c-kit+, s-100-, desmin-, and smooth muscle antigen-. We completed surgical resection using the transanal route. The final diagnosis was rectal gastrointestinal stromal tumor.