Iron deficiency anemia is the most common hematologic disease of infancy and childhood. Iron deficiency anemia caused by hemangioma of the small intestine is uncommon. We report a case of a five-year-old boy with iron deficiency anemia which was not improved with oral iron supplement therapy for over two years. The cause of anemia has not been clarified by previous studies. We discovered a cavernous hemangioma of the small intestine and the patient completely recovered from anemia with the resection of hemangioma.