Distinguishing intradural extramedullary (IDEM) spinal ependymoma from myxopapillary ependymoma is challenging due to the location of IDEM spinal ependymoma. This study aimed to investigate the utility of clinical and MR imaging features for differentiating between IDEM spinal and myxopapillary ependymomas. We compared tumor size, longitudinal/axial location, enhancement degree/pattern, tumor margin, signal intensity (SI) of the tumor on T2-weighted images and T1-weighted image (T1WI), increased cerebrospinal fluid (CSF) SI caudal to the tumor on T1WI, and CSF dissemination of pathologically confirmed 12 IDEM spinal and 10 myxopapillary ependymomas. Furthermore, classification and regression tree (CART) was performed to identify the clinical and MR features for differentiating between IDEM spinal and myxopapillary ependymomas. Patients with IDEM spinal ependymomas were older than those with myxopapillary ependymomas (48 years vs. 29.5 years, p < 0.05). A high SI of the tumor on T1W1 was more frequently observed in IDEM spinal ependymomas than in myxopapillary ependymomas (p = 0.02). Conversely, myxopapillary ependymomas show CSF dissemination. Increased CSF SI caudal to the tumor on T1WI was observed more frequently in myxopapillary ependymomas than in IDEM spinal ependymomas (p < 0.05). Dissemination to the CSF space and increased CSF SI caudal to the tumor on T1WI were the most important variables in CART analysis. Clinical and radiological variables may help differentiate between IDEM spinal and myxopapillary ependymomas.