Background. Although the therapeutic outcome for acquired aplastic anemia has improved markedly with the introduction of immunosuppressive therapy using anti-thymocyte globulin and cyclosporine, a significant proportion of patients subsequently relapses and requires second line therapy. However, detailed analyses of relapses in aplastic anemia children are limited. Design and Methods. We previously conducted two prospective multicenter trials of immunosuppressive therapy for children with aplastic anemia: AA-92 and AA-97 that began in 1992 and 1997, respectively. In this study, we assessed the relapse rate, risk factors for relapse, and the response to second line treatment in aplastic anemia children treated with anti-thymocyte globulin and cyclosporine. Results. From 1992 to 2007, we treated 441 aplastic anemia children with standard immunosuppressive therapy. Among the 264 patients who responded to immunosuppressive therapy, 42 (15.9%) relapsed. The cumulative incidence of relapse was 11.9% at ten years. Multivariate analysis revealed that relapse risks were significantly associated with an immunosuppressive therapy regimen using danazol (relative risk, 3.15; P = 0.001) and nonsevere aplastic anemia (relative risk, 2.51; P = 0.02). Seventeen relapsed patients received additional immunosuppressive therapy with anti-thymocyte globulin and cyclosporine. Eight patients responded within six months. Seven of nine non-responders to second immunosuppressive therapy received hematopoietic stem cell transplantation and five are alive. Eleven patients directly underwent hematopoietic stem cell transplantation and 7 are alive. Conclusions. In the present study, the cumulative incidence of relapse at ten years was relatively low compared with other studies that mainly consisted of adult patients. To establish optimal therapy for these patients, a multicenter prospective study is warranted.