Sunitinib, a molecular-targeted therapy, is a potential new treatment strategy for malignant pheochromocytoma. However, because of the rarity of malignant pheochromocytoma and the consequent limited number of patients available for clinical study, there is no good evidence of the efficacy of sunitinib for malignant pheochromocytoma. The present report describes our experience with sunitinib for refractory malignant pheochromocytoma. Two patients were treated with sunitinib at a standard dose (50 mg daily; 4 weeks on, 2 weeks off) after cyclophosphamide/vinblastine/dacarbazine chemotherapy, because vascular endothelial growth factor (VEGF)-positive cells were partly observed by immunohistochemical staining. Both patients were assessed as having stable disease according to the Response Evaluation Criteria in Solid Tumors 1.1. The duration of overall survival from the time sunitinib was initiated was 13 and 8 months, respectively, and the progression-free survival was 5 and 4 months, respectively. Adverse events were evaluated according to the Common Terminology Criteria for adverse events of the US Department of Health and Human Services version 4.0. One patient experienced hypothyroidism (Grade 2) and thrombocytopenia (Grade 2). The other patient experienced anorexia (Grade 3) and general malaise (Grade 3). In conclusion, sunitinib was effective in the treatment of malignant pheochromocytoma when VEGF-positive cells were observed in the tumor specimens.