Omenn syndrome (OS) is typically observed in the autosomal recessive form of severe combined immunodeficiency (SCID) with autoreactive manifestations, and it requires allogeneic hematopoietic stem cell transplantation. Unlike non-OS SCID, a conditioning regimen is usually required to eradicate T-cells; however, optimal conditioning regimens are not established mainly because of the rarity of OS. Here, we report a case of hematopoietic stem cell transplantation with a reduced dose of busulfan, as a conditioning regimen and successful engraftment with complete chimerism. OS was diagnosed in a one-month-old boy based on a diffuse erythematous rash, absent B-cells, and activated T-cells. Genetic analysis failed to identify causative mutations for OS/ SCID, such as RAG1/2. Bone marrow transplantation was performed from his HLA-matched sister with a conditioning regimen consisting of targeted busulfan, fludarabine, and anti-thymocyte globulin. Cyclosporine had been administered before transplantation to control abnormal T-cell activation and continued for graft-versushost disease (GVHD) prophylaxis. Engraftment was achieved on day 12, and no GVHD symptoms were observed. For stem cell transplantation for OS, prior control of autoreactive symptoms with immunosuppressants is important for safe transplantation and reduced intensity conditioning (RIC) can be an option to achieve sustained engraftment.