Abstract We report the case of a patient with a giant Brunner's gland hamartoma that was pathologically diagnosed by endoscopic mucosal resection. A 69‐year‐old woman presented with intermittent abdominal pain, and imaging revealed a smooth saccular submucosal tumor, 40 mm in diameter, on the anterior wall of the duodenal bulb. Brunner's gland and smooth muscle tissue were observed on endoscopic ultrasound‐guided fine‐needle aspiration biopsy, which resulted in the preoperative diagnosis of a duplication cyst. However, subsequent endoscopic mucosal resection established a final histopathological diagnosis of Brunner's gland hamartoma.