Hematopoietic Stem Cell Transplantation (HSCT) is a curative treatment for certain blood disorders, but can lead to complications such as Autoimmune Cytopenia (AIC), particularly Autoimmune Hemolytic Anemia (AIHA). AIHA after HSCT often involves donor-derived antibodies attacking donor red blood cells, but this case report describes a unique case in a 7-year-old male with beta-thalassemia major. Following HSCT, he developed AIHA nine months after transplantation from an unrelated donor. Despite initially successful engraftment, chimerism analysis revealed a decline in donor cells coincident with the onset of AIHA. The patient had severe hemolysis, a positive Direct Coombs Test (DAT) for IgG and C3d, and several antibodies including anti-e, anti- C, and anti-D. Treatment with cyclosporine and prednisone initially stabilized his condition, but discontinuation resulted in relapse, worsening chimerism, and increased antibody titers. Analysis confirmed the predominance of recipient immune cells, suggesting that AIHA was driven by the recipient's immune response against his own red blood cells. This case emphasizes the complexity of immune reconstitution after HSCT and highlights a recipient-versus-recipient mechanism in post-transplant AIHA.