We describe a case in which segmental resection of the third portion of the duodenum was performed for a gastrointestinal stromal tumor (GIST). A 31-year-old woman was found to have a 3.5 cm hypovascular tumor at the posterior inferior aspect of the pancreatic head. Preoperative duodenal biopsy revealed that the tumor was positive for c-kit and vimentin, and was diagnosed as a duodenal GIST. Segmental resection of the third portion of the duodenum with papilloplasty and duodenojejunostomy was carried out and there were no postoperative complications. Pancreatoduodenectomy is not always necessary in the treatment of a duodenal GIST. This duodenectomy procedure can serve as a less extensive resection for a duodenal GIST located in the third portion of the duodenum.