We report a case of immune-mediated myelopathy occurring 4 months after unrelated bone marrow transplantation for myelodysplastic syndrome. After the tapering of cyclosporine for graft-versus-host disease prophylaxis, the patient developed several neurological symptoms mimicking the clinical features of multiple sclerosis (MS). Although neurological exacerbation was well stabilized with a bulk dose of corticosteroid, sustained improvement of neurological deficits occurred after the patient developed hematopoietic mixed chimerism (HMC). This experience may provide clinical evidence supporting the current therapeutic concept, in which HMC induction can potentially cure several immune diseases, including MS.