A male infant, aged 1 month and 24 days, was diagnosed with immune thrombocytopenia (ITP) and autoimmune hemolytic anemia (AIHA). Whole-exome gene sequencing revealed compound heterozygous mutations of LRBA, confirming a diagnosis of LRBA deficiency with an ALPS-like phenotype. Despite treatments with corticosteroids, neonatal-like exchange transfusions, rituximab, and sirolimus, the ALPS-like symptoms persisted and were complicated by pulmonary infection and cytomegalovirus viremia. At 3 months of age, the patient underwent haploidentical hematopoietic stem cell transplantation (HSCT) using bone marrow from his father. Post-transplantation, successful engraftment of platelets and granulocytes was achieved, infections were controlled, and no severe complications occurred. Three months after transplantation, the infant developed grade Ⅱ skin graft-versus-host disease (GVHD), which resolved completely following treatment. Currently, more than 8 months after transplantation, the patient remains healthy with normalized immune function and no recurrence of the ALPS-like phenotype. This article retrospectively analyzed a case of a young patient with LRBA deficiency and an ALPS-like phenotype, evaluating the efficacy and safety of HSCT using bone marrow-derived hematopoietic stem cells from a haploidentical father. The study indicates that for children unresponsive to first-line treatments, HSCT should be considered as early as possible. In the absence of a fully matched donor, haploidentical donors and bone marrow-derived stem cells represent viable options that may enhance engraftment, reduce GVHD and infection risks, and improve transplantation outcomes. Further studies are required to optimize the treatment protocol and improve prognosis.