Gastrointestinal stromal tumors are the most common subepithelial tumors of the gastrointestinal tract. Gastrointestinal stromal tumors are commonly detected in the stomach followed by the small intestine. Surgery for gastrointestinal stromal tumors affecting the duodenojejunal junction is technically challenging because of the anatomical complexity of this area. A 56-year-old woman visited the outpatient clinic with the chief complaint of melena associated with dizziness from 5 days ago. Abdominal computed tomography revealed an enhancing small bowel mass measuring 4 cm × 5 cm in the left upper abdomen abutting the duodenojejunal junction. She underwent successful laparoscopic small bowel segmental resection of the duodenojejunal junction area. Laparoscopic segmental resection with side-to-side duodenojejunostomy for a gastrointestinal stromal tumor at the duodenojejunal junction is an advanced and challenging procedure requiring experience and a good surgical technique.