We evaluated the outcome of children and adolescents with acquired severe aplastic anemia (SAA) who received haploidentical hematopoietic stem cell transplantation (HHCT) with in vitro T cell-depleted peripheral blood stem cells. Twelve patients with acquired SAA received a total of 15 HHCTs with in vitro CD3-depleted grafts between July 2009 and July 2012. Among the 12 patients, 11 achieved neutrophil engraftment at a median of 10 days (range, 9 to 13 days) after HHCT. One patient failed to achieve primary engraftment, and two experienced graft rejection soon after engraftment. All three patients who experienced early graft failure received a second HHCT and achieved sustained engraftment. Thus, the final engraftment rate was 100%. Acute graft-versus-host disease was assessed in nine patients, excluding the three patients with early graft failure. Three of these patients developed acute graft-versus-host disease (two ≥ grade II and one with grade III). All 12 patients survived and were transfusion-independent at a median follow-up of 14.3 months (range, 4.1 to 40.7 months). Hematopoietic stem cell transplantation from haploidentical family donors with in vitro CD3 T cell depletion is a reasonable therapeutic option for children and adolescents with acquired SAA. Our future trial with a uniform protocol will help to solve the problems associated with HHCT and provide a valuable platform for the further development of HHCT as a therapy for SAA.