Extragonadal germ cell tumors rarely arise from the brain stem. In this report, the authors present a rare case of germinoma developing in the medulla oblongata. A 31-year-old woman complained of intractable hiccups, hoarseness, and swallowing disturbance. Magnetic resonance imaging showed a tumor located on the dorsal part of the medulla oblongata without any abnormalities in the pineal body and suprasellar regions. Histological diagnosis of surgically resected tumor was germinoma. Tumor cells were positive for alkaline phosphatase, c-kit, octamer-binding transcription factor 3/4, cytokeratin, and epithelial membrane antigen in immunohistochemistry. The patient received adjuvant chemotherapy and irradiation to the residual tumor and cerebral ventricles. The patient is alive without recurrence 6 months after the surgery.