This study aimed to identify prognostic factors and describe the treatment outcomes of multidrug therapy in dogs with meningoencephalomyelitis of unknown etiology (MUE). A total of 23 dogs diagnosed with MUE were treated with prednisolone in combination with cyclosporine, cytosine arabinoside (CA), leflunomide, and mycophenolate mofetil. Based on the survival time, these dogs were divided into two groups: group A (n = 10), surviving for < 100 days, and group B (n = 13), surviving for > 100 days. Signalment, seizure activity, cerebrospinal fluid (CSF) analysis results, and magnetic resonance (MR) imaging findings were reviewed. Survival studies were conducted to investigate the association of each prognostic factor and treatment with the clinical outcome. There were no significant differences in age, sex, body weight, occurrence of seizures, cell number and protein concentration in the CSF, or location of lesions between groups A and B. Abnormal MR features were more frequently observed in group A than in group B. It was identified that the longest median survival time was administration of multi-drug therapy including CA. In conclusion, abnormal MR features were associated with poor prognosis in dogs with MUE and CA-based multi-drug therapy could be considered the most effective treatment of MUE.