Intramedullary ependymal cysts are exceedingly rare lesions, and have been previously reported in the literature as case reports. The aim of this study was to discuss the clinical presentation and the outcomes of microsurgery for these benign lesions. The authors retrospectively reviewed the records of ten patients who underwent microsurgery for intramedullary ependymal cysts. All patients had preoperative and postoperative magnetic resonance imaging. The surgical treatment included gross total resection and biopsy plus a cyst-subarachnoid shunt. The diagnosis of intramedullary ependymal cysts was based on radiological and pathological criteria. All patients were followed up, with a mean duration of 47.6 months. Intramedullary ependymal cysts were hypointense on T1-weighted images and hyperintense on T2-weighted images. Contrast-enhanced T1-weighted images showed no enhancement. Gross total resection was achieved in one case. Biopsy of the cyst wall plus cyst-subarachnoid shunt placement was achieved in nine cases. Long-term neurological function was improved in eight patients. No recurrence was observed on magnetic resonance imaging. Ependymal cysts should be considered in the differential diagnosis of intramedullary cysts. For symptomatic patients, early surgery should be performed before neurological deficits deteriorate. Complete decompression and cyst-subarachnoid shunt placement is the optimal treatment and the outcome may be favorable.