The use of mycophenolate mofetil (MMF) for a variety of immune‐mediated diseases in veterinary medicine has been described. However, there is only a small number of cases documenting its use in dogs with meningoencephalomyelitis of unknown aetiology (MUE). We hypothesized that the use of MMF and corticosteroids in dogs with MUE results in comparable survival data to other published treatment protocols and is associated with limited adverse effects. A retrospective study of medical case records of dogs clinically diagnosed with MUE recorded signalment, neuroanatomic localization, magnetic resonance imaging findings, cerebrospinal fluid analysis results, medications administered, follow‐up neurologic examinations, survival and adverse events. Variables were compared between dogs which were treated with MMF within 30 days of diagnosis (immediate group) vs. dogs in which MMF therapy was started >30 days after diagnosis (delayed group). Twenty‐five cases of MUE were identified. The overall median survival time from diagnosis was 731 days (range 43–1672 days). After 1 month of MMF treatment, 92% of dogs showed improvement on a neurological examination. There was no significant effect of any recorded parameter on survival, including delayed vs. immediate initiation of MMF treatment. Dogs with delayed treatment had significantly lower clinical remission rates than dogs with immediate treatment at 6 months after starting MMF. Adverse events were identified in two cases (8%) and were characterized by mild gastrointestinal signs (vomiting and decreased appetite). Administration of MMF appears safe in dogs with MUE. The use of MMF results in comparable survival times to alternate immunosuppressive protocols.