A 6-year-old boy was diagnosed with FLT3-ITD+acute monoblastic leukemia (AMoL). He showed resistance to 2 cycles of induction chemotherapy with etoposide, cytarabine, and mitoxantrone or idarubicin performed according to the Japan Pediatric Leukemia/Lymphoma Study Group (JPLSG) AML-05 protocol. His condition was also refractory to salvage FLAI-GO (fludarabine, cytarabine, idarubicin, and gemtuzumab ozogamicin) chemotherapy. Sequential administration of sorafenib at doses of up to 300 mg/day resulted in the first remission. He underwent bone marrow transplantation from his HLA 2-locus mismatched father. Recurrence was observed on post-transplantation day 71. A sustained partial response was observed after alternate-day readministration of sorafenib 150mg/day. In spite of a donor lymphocyte infusion, his blast cell count increased on day 245. Chemotherapy with an increased dose of sorafenib reduced the blast cell count. Although a second HLA-mismatched allogeneic peripheral blood stem cell transfusion was performed, the patient died of regimen-related toxicity. Herein, we report a pediatric case of primary refractory FLT3-ITD+ AMoL. Further prospective studies are necessary to validate the efficacy of sorafenib treatment.