We experienced a case of a persistent trophoblastic disease associated with gradually progressive Brown-Sequard syndrome, which was found to be due to a primary intramedullary spinal cord germinoma with syncytiotrophoblastic giant cells (STGC). We performed both chemotherapy and radiotherapy on separate occasions. Although the chemotherapy appeared to be ineffective, radiotherapy resulted in the disappearance of spinal cord lesions for four years. We reported a case of intramedullary spinal cord germinoma with STGC for which radiotherapy was a better therapeutic modality.