Perforin deficiency characterized by markedly reduced cytotoxic T and natural killer cell activities is one type of familial hemophagocytic lymphohistiocytosis (FHL). FHL is a fatal inherited disease, and treatment with stem cell transplantation has resulted in a normal activity of killer cells. We herein report a case of FHL with perforin deficiency that was primarily treated by the administration of liposteroid to reduce hypercytokinemia. Thereafter, allogenic bone marrow transplantation with nonmyeloablative conditioning was successfully performed without any adverse effects on the patient's physical or developmental status. These observations suggest that this treatment strategy might thus be recommended in infants with FHL to reduce treatment-related complications, especially in patients with relatively mild clinical courses.