Patients with symptomatic gastrointestinal stromal tumor (GIST) typically present with gastrointestinal bleeding and abdominal pain. This report presents an unusual case of fundic GIST complicated by gastroduodenal intussusception, manifesting as acute pancreatitis. The patient presented with epigastric pain and pancreatic enzyme elevation; thus, he was diagnosed with acute pancreatitis. Computed tomography showed evidence of pancreatitis and a 4×4.7 cm well-defined hyperdense lesion in the 2nd part of the duodenum, compressing the pancreatic head and pancreatic duct. Esophagogastroduodenoscopy revealed invagination of the gastric folds into the duodenum, causing pyloric canal blockage consistent with gastroduodenal intussusception. Spontaneous reduction of the lesion during endoscopy revealed a 4 cm pedunculated subepithelial mass with central ulceration originating from the gastric fundus. Endoscopic ultrasound demonstrated a heterogeneous hypoechoic lesion originating from the 4th layer of the gastric wall. Laparoscopic-endoscopic intragastric wedge resection of the fundic lesion was subsequently performed, and surgical histology confirmed GIST.