Primary mucosal melanomas of the head and neck are rare. In addition, second primary mucosal melanoma following primary cutaneous malignant melanomas is very rare. We report a second primary mucosal melanoma. A 76-year-old woman, who had a previously cutaneous malignant melanoma of the left foot, visited with a complaint of a foreign body sensation of the throat. Endoscopy revealed a black mass at the left piriform sinus of the hypopharynx. After wide surgical excision of the lesion and reconstruction with a radial forearm free flap, the histopathology was confirmed to be a second primary mucosal malignant melanoma of the hypopharynx. Five months postoperatively, masses were palpated in the neck, and metastasis was diagnosed. The patient was treated with adjuvant chemotherapy and radiotherapy. Eight months postoperatively, computed tomography scans showed other metastatic masses in the liver, spleen, both adrenal glands, soft tissues of the abdominal wall, and both lungs. After that, the patient died 9 months postoperatively. We report a rare case of second primary mucosal malignant melanoma of the hypopharynx. Although rare, this case shows that a detailed examination of the hypopharynx and the head and neck should be a part of the follow-up examination in all cutaneous malignant melanoma patients.