Haploidentical hematopoietic cell transplantation (HCT) conditioning with clofarabine and target area under the blood concentration-time curve (AUC)-based busulfan adjustment was performed in three patients with refractory pediatric leukemia. The target AUC for two patients who had already received multiple transplantations was 3600 and 4000 μmol min/L, and that for the patient with Down's syndrome was 3000 μmol min/L. Regimen-related toxicity was well tolerated in all cases. All three maintained cytological remission throughout the follow-up period (between 31 and 167 weeks). Thus, haploidentical HCT conditioning with clofarabine and target AUC-based busulfan adjustment may be a preferable option for children with recurrent or refractory pediatric leukemia.