We report a 14-year-old boy with X-linked agammaglobulinemia (XLA) complicated by isolated non-progressive myelitis caused by Coxsackie virus B1. Despite the absence of immunoglobulin supplement and persistence of the virus for the initial 2 years, motor impairment did not show any progression for 3 years. This report shows that the prognosis of central nervous system infection in XLA is not determined by immunoglobulin levels alone, and that it is not always progressive or fatal. The balance between host immunity and the virulence of the causative virus may be involved in the prognosis of meningoencephalitis in XLA.