We herein report a rare case of primary malignant urethral melanoma developed in an elderly Japanese patient with hypertension, diabetes and hyperlipidemia. An 80-year-old female presented at our hospital with a history of urodynia and perineal pain lasting for several months. Cystoscopy revealed cystitis and urethritis with erosion. At that time, urinary cytology was negative for malignancy, although melanophages were observed. Four months later, lower abdominal computed tomography and magnetic resonance imaging indicated urethral tumors. Urinary cytology subsequently detected malignant melanoma, and a biopsy of the urethra confirmed malignancy. Although inguinal lymph node metastasis was found 16 months postoperatively, the patient has remained free of disease for more than six years after surgery and chemotherapy.