We report on a boy diagnosed with germinoma with syncytiotrophoblast giant cells located near the pineal gland. He initially received induction chemotherapy and radiotherapy to the tumor and the third ventricle, but the disease soon recurred along the spine. Thereafter, radiation to the whole craniospinal axis was performed. Sixteen months later, the pineal tumor recurred, and traditional chemotherapy, radiosurgery, and high-dose chemotherapy were applied as salvage treatments. However, the patient eventually had another relapse and passed away with an overall survival duration of 45 months. In conclusion, germinoma with syncytiotrophoblast giant cells may have a poor prognosis and aggressive treatment is necessary.