Synchronous spinal intramedullary ependymal cysts and intramedullary schwannomas are rare. To the best of our knowledge, the present study is the first report of a case of intramedullary schwannoma coexisting with an ependymal cyst. A 35-year-old male presented with lower back pain and weakness in the left leg. Magnetic resonance imaging identified an intramedullary cystic-solid lesion at the thoracolumbar junction of T11-L2; based on the clinical presentation and radiological features, a pre-operative diagnosis of ependymoma was formed. Subsequently, the patient underwent a T11-12 laminectomy via a posterior approach, with intraoperative monitoring of somatosensory and motor-evoked potentials, achieving a gross total resection of the tumor with a well-demarcated dissection plane. Post-operative histopathological examination demonstrated a schwannoma coexisting with the ependymal cyst, and the neurological status of the patient markedly improved compared with the pre-operatively observed neurological deficit.