We report the case of a 33-year-old man with diplopia, sleepiness, and paresthesia of the left upper limb that were slowly progressive. On admission, he presented with restriction in the vertical movement of the eyes and abduction of the right eye, and horizontal and convergence nystagmus. Slight weakness of the left upper limb, bilateral Babinski sign, and truncal ataxia were also noted. Cerebral magnetic resonance imaging was performed, and gadolinium-enhanced T1-weighted imaging revealed a mass lesion that involved the diencephalon and the corpus callosum, which was invariably enhanced. Specimens obtained using a brain biopsy showed epithelioid granuloma with the presence of foreign body giant cells and lymphocytic infiltration. Prednisolone was administrated because we suspected neurosarcoidosis, but the clinical symptoms worsened with the enlargement of the lesion. A re-evaluation of the biopsy specimens using immunohistochemistry revealed tumor cells of germinoma that were scattered among the lymphocytes and positive for periodic acid-Schiff staining, placental alkaline phosphatase, and c-kit. A combination of chemotherapy and radiation resulted in clinical improvement and marked reduction of the mass lesion in size. We concluded that the possibility of germinoma should be considered in case granulomatous inflammation is observed in brain biopsy specimens.