We herein report a rare case of ectopic pancreatic acinar cell carcinoma (ACC) which presented as a submucosal tumor of the pylorus. A 73-year-old man came to our hospital presenting with epigastralgia. Esophago-gastroduodenal endoscopy showed no mucosal lesions, but a submucosal tumor was observed around the pylorus. Abdominal computed tomography revealed two round masses. One was located in the pylorus, while the other was found between the portal vein and the inferior vena cava. An examination of a biopsy specimen was inconclusive. We diagnosed a gastrointestinal stromal tumor or malignant lymphoma preoperatively, and decided to perform an operation in order to confirm the diagnosis and select the optimal treatment. Intraoperatively, the mass in the pylorus invaded the pancreatic head, and the lymph node in the hepatoduodenal ligament was swollen. We performed a pancreaticoduodenectomy as a radical excision. The resected specimen showed the 7.6 x 4.9-cm size tumor to mainly originate from the pylorus. Histopathologically, the tumor was identified as pancreatic ACC with lymph node metastasis. The tumor cells were labeled by immunohistochemical staining for alpha1-antitrypsin. Because of the tumor location, we considered the tumor to have originated from the ectopic pancreatic tissue in the stomach. This is only the second case of ACC originating from an ectopic pancreas reported in the literature.