We herein report the case of a 39-year-old man who developed bilateral auricular chondritis, conjunctivitis, and central neurological symptoms. He was diagnosed with encephalitis associated with relapsing polychondritis (RP) based on the findings of an ear cartilage biopsy, cerebrospinal fluid examination and magnetic resonance imaging. Although oral prednisolone (60 mg/day) was administered, the initial steroid therapy did not improve his symptoms. In contrast, methylprednisolone (mPSL) pulse therapy followed by prednisolone gradually ameliorated his condition. There were no episodes of recurrence during the two-year follow-up period. A review of the literature revealed that meningoencephalitis and encephalitis are rare, but important, complications of RP responsive to mPSL pulse therapy.