We report a case of a 72-year-old woman who initially presented with symptoms of bulbar myasthenia and was positive for anti-acetylcholine receptor antibodies. She subsequently developed painful muscle spasms, myoclonus, and stiffness. Thymoma was detected, and both anti-glycine receptor and anti-glutamic acid decarboxylase antibodies were found. She was diagnosed with thymoma-associated progressive encephalomyelitis with rigidity and myoclonus (PERM). She experienced marked improvement after thymectomy followed by plasma exchange and intravenous immunoglobulin and prednisolone. This case suggests that thymectomy followed by sufficient immunosuppression may be useful in the treatment of thymoma-associated PERM. Myasthenia gravis may develop in thymoma-associated PERM patients.