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Preoperative imatinib treatment for rectal gastrointestinal stromal tumors (GISTs) has been reported to reduce the tumor size and help preserve the anal sphincter function. On the other hand, preoperative imatinib may prevent an accurate assessment of the recurrent risk. The endoscopic resection of rectal GIST is rarely reported because of challenges that include securing the visual field and avoiding perforation. This paper reports a case in which a 5.5×4.0 cm sized rectal GIST was treated effectively by an endoscopic submucosal dissection (ESD) without preoperative imatinib. To date, the patient had no tumor recurrence or complications and is receiving adjuvant imatinib treatment. This case shows that ESD may be a good treatment option to preserve the anus in rectal GIST treatment.