Introduction Gastrointestinal stromal tumors of the duodenum are uncommon. They can reach a large size. Diagnosis can be elusive and managing them can be difficult. Our case report aims to increase awareness and highlight some issues related to the diagnosis and management of duodenal gastrointestinal stromal tumors. Case presentation We present the case of a 38-year-old Middle Eastern woman with a large, slowly-growing gastrointestinal stromal tumor of the duodenum. Her complaints were minor epigastric discomfort and swelling. A pancreaticoduodenectomy with complete tumor excision was performed. She was doing very well with no evidence of disease recurrence when she was last seen 34 months after her operation. Conclusion Gastrointestinal stromal tumors of the duodenum should be suspected in any patient with a duodenal wall mass. Extramural growth and central ulceration with or without bleeding should alert the endoscopist to the possibility of a duodenal gastrointestinal stromal tumor diagnosis. There is more than one surgical approach available; however, complete surgical excision, with negative margins, is the absolute requirement. Preoperative imatinib mesylate can be considered in unresectable or borderline resectable cases.