Duodenal gastrointestinal stromal tumors (GISTs) are uncommon and a relatively small subset of GISTs whose optimal surgical procedure has not been well defined. Because submucosal spread and local lymph node involvement is infrequent in GISTs, wide margins with routine lymph node dissection may not be required. Various techniques of limited resection for duodenal GISTs have been described depending on the site and the size of the tumors. In this study, we report two cases of GIST involving the third and fourth portion of the duodenum successfully treated by segmental duodenectomy with end-to-end duodenojejunostomy. This technique should be considered as a treatment option for GIST located at the third and fourth portion of the duodenum.