A 95-year-old Japanese woman presented to our hospital with intermittent vomiting and several episodes of melena. Abdominal computed tomography revealed intussusception of the gastric tumor into the duodenum. After endoscopic reduction, endoscopic ultrasonography identified a hypoechogenic lesion limited to the submucosal layer. Endoscopic resection was performed as a localized treatment for the prevention of recurrent gastroduodenal intussusception. To our knowledge, there have been no other reports describing a gastric gastrointestinal stromal tumor presenting with gastroduodenal intussusception and treated using an endoscopic submucosal dissection technique.