A 4-year-old girl with familial hemophagocytic lymphohistiocytosis (FHL) underwent unrelated cord blood stem cell transplantation (uCBSCT) using the fludarabine-based non-myeloablative conditioning regimen. Shortly after the uCBSCT, she experienced the reactivation of the FHL, and subsequent graft failure. Considering that the residual recipient lymphocytes, which survived after non-myeloablative conditioning, had a role in the FHL reactivation and in the graft rejection, myeloablative conditioning combined with horse ATG was used to eradicate the recipient lymphocytes in the second CBSCT. Furthermore, in order to prevent rejection, cord blood, the DNA type of which was completely matched in a host to graft (HVG) direction, was selected. In the second uCBSCT, FHL reactivation was noted at a limited level. Complete chimerism was achieved and the NK-cell activity recovered to the normal range. Our case suggests the necessity of the conditioning regimen to eradicate host lymphocytes in the stem cell transplantation for FHL, and the significance of HLA DNA-typing in uCBSCT for pediatric patients.