Pyogenic granuloma is a lobular capillary hemangioma that occurs mostly on the skin, and occasionally on the mucosal surface of the oral cavity, but very rarely in the gastrointestinal tract. We report the case of a 63-year-old woman who suffered from palpitations, and iron deficiency anemia for 5 years. Esophagogastroduodenoscopy and colonoscopy could not reveal significant bleeding focus. She had not received medical treatment except for oral iron. Capsule endoscopy revealed a bleeding focus in the small intestine. Afterwards, we carried out double balloon endoscopy to treat the lesion. We found a subpedunculated polyp in the small intestine at 100 cm away from ileocecal valve by double balloon endoscopy and resected it endoscopically. The histological features of the polyp were consistent with pyogenic granuloma. Anemia had improved gradually without giving oral iron after polypectomy.