This report describes a case of agammaglobulinemia with progressive encephalitis. The patient was a 6-year-old male who was diagnosed as having Bruton-type agammaglobulinemia at age 6 months. After the diagnosis was made, he received monthly intravenous immunoglobulin replacement with a residual immunoglobulin G level of more than 400 mg/dL. At 5 years of age, he presented with symptoms of mental deterioration and gait disturbance. He had no history of infection of the central nervous system. Brain biopsy revealed CD8-positive T-cell infiltration with cortical damage, but no infectious agents were observed by either immunohistochemistry or virus isolation. Treatment with subcutaneous interferon-alpha and high-dose intravenous immunoglobulin was begun, and clinical symptoms improved within a month. Hence, patients with agammaglobulinemia should be carefully monitored for complications of the central nervous system even if there is no history of infection.