We report here the case of a suprasellar cystic germ cell tumor (GCT) initially diagnosed as an arachnoid cyst. A 10-year-old boy experienced headache, dizziness, and diplopia, and was shown to have an approximately 2 cm suprasellar cyst. Two months after endoscopic third ventriculostomy was performed, a 5-6 cm cystic mass with an internal enhancing component was observed in the suprasellar cistern. Serum human chorionic gonadotropin levels were slightly increased in the serum and cerebrospinal fluid (55 and 162 IU/L, respectively) but were strikingly elevated in the cystic fluid (14,040 IU/L). The patient showed complete remission, with only a very small cystic lesion remaining after surgery, chemotherapy, and radiation treatment for a suprasellar mixed GCT. However, follow-up after treatment was complicated by moyamoya syndrome and cerebral infarction. GCT can be considered as a rare differential diagnosis in the case of a suprasellar cystic mass. Evaluation of tumor markers and close follow-up will be necessary.