Primary germ cell tumors of the central nervous system (CNS) typically occur in the neurohypophysis, hypothalamus, or pineal gland and rarely in the spinal cord. We report a case of a spinal intramedullary tumor, which was first detected on magnetic resonance imaging (MRI) 41 months after the initial symptoms, with a verified pathological diagnosis of germinoma. The initial symptom was an abnormal sensation in the left plantar region that gradually worsened, resulting in severe sensory disturbance, difficulty in standing, and even bladder rectal disturbance. Repeated MRI after the onset failed to provide an imaging diagnosis. The MRI was performed 41 months after the onset and revealed a previously undiagnosed, contrast-enhancing spinal intramedullary neoplastic lesion at the Th11-12 level. Gross total resection of the tumor was successfully performed, and the pathology confirmed the diagnosis of pure germinoma. Postoperative chemotherapy, followed by local radiation, was successfully administered. Among primary germinomas of the CNS, occult germinoma that lacks imaging findings suggestive of tumors in the early stages of onset and becomes apparent over time is often reported as a primary neurohypophyseal germinoma, particularly in adolescents presenting with diabetes insipidus. In the present case, the lesion appeared to correspond to a primary occult germinoma of the intramedullary spinal cord.