Ectopic pancreas is an uncommon congenital anomaly, which is usually found incidentally in clinical practice. It presents with nonspecific gastrointestinal symptoms like epigastric pain and dyspepsia and rarely with the clinical findings of obstructive jaundice or intestinal obstruction, or it may mimic gastrointestinal system cancer. Herein, we describe a case of ectopic pancreas in the duodenum, which was the cause of the intractable diarrhea. In our patient, upper gastrointestinal endoscopy and endoscopic ultrasonography revealed a 1.5 cm submucosal lesion, which was umbilicated centrally with a normal in appearance overlying mucosa. Endoscopic biopsy of the lesion was normal. Pathological examination of the lesion after surgical excision was compatible with ectopic pancreas. After total excision of the lesion, the clinical findings of the patient normalized. Ectopic pancreas presenting with diarrhea has not been reported previously in the literature.