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Gastrointestinal stromal tumor (GIST) commonly occurs in the stomach. We would like to report an uncommon presentation of gastric GIST with gastroduodenal intussuception. A patient with known history of gastric GIST at fundus for 10 years presented to the casualty department with recurrent epigastric pain, deranged liver function, and hyperamylasemia. Computed tomography of the abdomen showed intussuception of the gastric GIST into duodenum. Emergency operation with synchronous endoscopic reduction and laparoscopic wedge resection was performed and patient had uneventful recovery. This simultaneous endoscopic and laparoscopic treatment should be considered for this rare complication of GIST.