This study aimed to compare the efficacy and safety between haploidentical hematopoietic stem cell transplantation (HHCT) and immunosuppressive therapy (IST) for the treatment of pediatric acquired severe aplastic anemia (SAA). The clinical data of 28 children with SAA treated from June 2010 to October 2014 at our hospital were retrospectively reviewed. Of these patients, 18 were treated with HHCT and 10 with IST. The median follow-up time was 23.5 months (range, 3–52 months). There was no significant difference in overall survival rate between the HHCT group and the IST group (66.7% vs. 70%, P > 0.05). Graft-versus-host disease occurred in 83.3% (15/18) of the HHCT group, including 5 cases with grade III or higher. In comparison with IST, HHCT has similar efficacy and safety profiles in the treatment of pediatric SAA.