It is insufficient to distinguish benign tumors from malignant pheochromocytoma using histological analyses of resected tissue alone. We experienced an 18-year-old woman who complained of severe headaches in whom hypertension was revealed. She was suspected of having a malignant tumor based on her clinical characteristics, despite showing no evidence of metastatic lesions. The patient was diagnosed with an aggressive form of hereditary pheochromocytoma-paraganglioma syndrome (HPPS) based on immunohistochemical analyses and genetic testing. The present case indicates that conducting genetic testing, including SDHB mutation analyses, is required to determine the prognosis in patients highly suspected of having HPPS.