Isolated central nervous system (CNS) relapse in acute myeloid leukemia (AML) rarely occurs later than 2 years after remission. We present a child diagnosed with AML (FAB M5) without CNS involvement at diagnosis who was treated with chemotherapy and consolidated with autologous hematopoietic stem cell transplantation. He was in complete remission for >6 years until he had an isolated CNS relapse. He was treated with only intrathecal chemotherapy and achieved a second complete remission, but relapsed in the bone marrow 5 months after the CNS relapse. Treatment of late isolated CNS relapse of AML is discussed.