A 41-year old man with nasopharyngeal adenoid cystic carcinoma （T4aN0M0） received carbon ion radiotherapy of 65 Gy （RBE） in 25 fractions. The treatment was well tolerated and complete response was obtained. At 30 months after the therapy, mucosal necrosis and brain necrosis were observed as a late toxicity. Despite treatment with oral steroid, brain necrosis worsened and osteonecrosis of the skull base and cervical spine was newly observed. The patient died of intracranial infection caused by mucosal necrosis, brain necrosis and osteonecrosis of the skull base and cervical spine at 54 months after the carbon ion radiotherapy. A pathological autopsy revealed no recurrence of adenoid cystic carcinoma. Carbon ion radiotherapy may be a useful treatment option for radioresistant malignant tumors of the head and neck. Optimal treatment planning and long-term careful follow-up are necessary to control fatal late toxicities.