A 64-year-old man was referred to our hospital for further management of anemia and duodenal tumor. Esophagogastroduodenoscopy (EGD) in our division showed a semipedunculated tumor, 7 mm in diameter, above the major papilla of the duodenum. The positional relationship between the tumor and the minor papilla of the duodenum was unclear. A biopsy led to the diagnosis of pyogenic granuloma. Contrast-enhanced computed tomography (CT) showed clear enhancement of the tumor. Endoscopic retrograde cholangiopancreatograpy (ERCP) showed no pancreas divisum. We performed endoscopic mucosal resection (EMR) of the tumor. Pathological examination of the resected tumor showed proliferation of blood capillaries within a stroma containing lymphocytic inflammatory cells and fibrosis. The surface of the tumor was covered with slough. These findings were most consistent with the diagnosis of pyogenic granuloma. Follow-up EGD after 3 months showed no signs of tumor recurrence, and the normal minor papilla of the duodenum was detected above the EMR scar. At the follow-up after 6 months, the patient remained in good general condition.