Allogeneic hematopoietic stem cell transplantation for severe aplastic anemia from an alternative donor is associated with higher risks of graft rejection and severe graft-versus-host disease. We developed a conditioning regimen consisting of rabbit anti-thymocyte globulin, fludarabine, cyclophosphamide, and low-dose total body irradiation. Two adult female patients with transfusion-dependent very severe aplastic anemia underwent 1-locus mismatched transplantation using this regimen. Both patients achieved stable engraftment and the clinical course thereafter was uneventful with persistently normal ovarian function. This novel conditioning regimen may be suitable for alternative donor transplantation for severe aplastic anemia, especially in young female patients.