A 62-year-old Japanese man presented to our hospital with a history of weight loss of 6 kg in 4 mo. Imaging examinations revealed a tumor located on the third portion of the duodenum with stenosis. We suspected duodenal carcinoma and performed pancreas-preserving segmental duodenectomy. Adenocarcinoma arising from a heterotopic pancreas at the third portion of the duodenum was finally diagnosed by immunohistochemical staining. Malignant transformation in the duodenum arising from a heterotopic pancreas is extremely rare; to our knowledge, only 13 cases have been reported worldwide, including the present case. The most common location of malignancy is the proximal duodenum at the first and descending portion. Herein, we describe the first case of adenocarcinoma arising from a heterotopic pancreas, which was located in the third portion of the duodenum, with a review of the literature. A 62-year-old Japanese man presented to our hospital with a history of weight loss of 6 kg in 4 mo. Imaging examinations revealed a tumor located on the third portion of the duodenum with stenosis. We suspected duodenal carcinoma and performed pancreas-preserving segmental duodenectomy. Adenocarcinoma arising from a heterotopic pancreas at the third portion of the duodenum was finally diagnosed by immunohistochemical staining. Malignant transformation in the duodenum arising from a heterotopic pancreas is extremely rare; to our knowledge, only 13 cases have been reported worldwide, including the most common location of malignancy is the proximal duodenum at the first and descending portion. Herein, we describe the first case of adenocarcinoma arising from a heterotopic pancreas, which was located in the third portion of the duodenum, with a review of the literature.