Background: Gastrointestinal stromal tumor (GIST) is a mesenchymal tumor originating in the wall of the gastrointestinal tract, and 20-30% of these tumors originate from the small intestine. The clinical manifestations of GIST of the small intestine generally include a palpable mass, distention, and abdominal pain and sometimes include acute abdomen due to ileus, bleeding, perforation, and intussusception at onset. Here, we describe a rare case of a pedunculated GIST of the small intestine complicated by torsion.Case presentation: A 69-year-old woman was referred for lower abdominal pain. Abdominal contrast-enhanced computed tomography showed a 73×62×57-mm tumor in the pelvic cavity with an enhanced margin and reduced contrast effect inside of it. T2-weighted magnetic resonance imaging showed a hyperintense, demarcated, lobulated tumor. The diffusion-weighted image showed hyperintensity, and the apparent diffusion coefficient value revealed diffusion restriction, indicating malignancy. T1-weighted images showed a low intensity tumor; contrast-enhanced images showed hypointensity inside of the tumor and slight hyperintensity around its edges. It was presumed that the tumor had caused hemorrhagic infarction. Emergency laparotomy was performed, and the pedunculated tumor was found to be twisted 360 degrees clockwise at the pedicle with hemorrhage and necrosis due to torsion. We performed partial resection of the small intestine including the tumor. Histopathology revealed tightly arranged spindle-shaped cells with hemorrhage, congestion, and inflammatory cell infiltration. Immunohistochemical staining showed positivity for CD34, CD117, and DOG1.Conclusions: The present report describes a very rare case in which pedicle torsion of an extra luminal expanding GIST of small intestine, although there were some reports of small intestine volvulus caused by GIST of small intestine as a rare condition. The torsion of pedunculated GIST of small intestine should be recognized as an emergency condition of GIST, and we report that characteristic findings of this condition were acquired with CT and MRI which was possibility useful for the diagnosis.