Heterotopic pancreas is defined as the presence of ectopic pancreatic tissue outside boundaries of the pancreas without vascular and duct system connection with the pancreas. Ectopic locations are mostly found anywhere in the gastrointestinal tract such as the stomach (24–38%), the duodenum (9–36%), and the jejunum (0.5–27%). Clinical manifestations are not specific, vague, and misdiagnosed another digestive disease. Most cases are incidentally detected by histological examination of specimens resected for different pathologies during endoscopy, surgery, or even autopsy. We report a case of a 31-year-old man who admitted to the hospital with the reason of epigastric pain for 3 days. Clinical examination showed mild epigastric tenderness. The past medical history of patient was unremarkable. A submucosal lesion was observed in the first part of the duodenum during endoscopy. Computed tomography and endoscopic ultrasonography findings were suspected to be heterotopic pancreatic tissue. After laparoscopic surgery for biopsy, it was histologically confirmed duodenal ectopic pancreas. It is difficult to differentiate gastrointestinal pancreatic heterotopia from gastrointestinal stromal tumors, leiomyoma, or lymphomas by using endoscopy because ectopic tissue is mostly located in the submucosal layer. In addition, rare cases of ectopic pancreatic tissue transform malignancy. Surgical treatment should be considered to take adequate tissue samples for biopsy or resect the lesions in symptomatic patients. Duodenal pancreatic heterotopia is an uncommon congenital malformation and most patients are asymptomatic. Histological examination is essential to exclude malignant lesions and to have an appropriate treatment.