BACKGROUND: Tumor-associated hypoglycemia can be caused by non-islet cell tumors including gastrointestinal stromal tumor (GIST) which is a rare paraneoplastic syndrome that leads to the release of insulin-like growth factor-2 (IGF-2). CASE PRESENTATION: We report the case of a 45-year old woman who was admitted to our hospital with refractory hypoglycemic episodes. We found normal serum insulin and c-peptide level and abdominal CT-scan showed a small duodenal wall lesion suggesting insulinoma. After tumor resection, hypoglycemia symptoms were recovered, but the pathological findings demonstrated the lesion was GIST. CONCLUSION: In a small gastrointestinal lesion with hypoglycemic symptoms we should consider IGF-II secreting GIST in addition to insulinoma.