Blood stream infection (BSI) is the most common infectious complication of hematopoietic stem cell transplantation (HSCT) and can cause substantial morbidity and mortality. Identification of risk factors for BSI might be helpful in efforts to reduce transplant-related death. This study analyzed the incidence of BSI and risk factors for BSI after transplantation in pediatric patients with aplastic anemia (AA). BSI occurred in 39 of 351 patients with AA (11.1%). Median onset of BSI was 8 days after transplantation (0 to 92 days). The 5-year overall survival rate was lower in patients with BSI (63.32±7.90%) than in patients without BSI (93.35±1.44%, p<0.0001). Univariate analysis showed that variables associated with BSI included history of immunosuppressive therapy with anti-thymocyte globulin, transplantation from unrelated donors, frequent blood transfusion before transplantation, major or major+minor mismatch of ABO blood type, graft versus host disease prophylaxis without cyclosporine and with tacrolimus, and long interval from diagnosis to transplantation. In these factors, long interval from diagnosis to transplantation was the only statistical significant factor for BSI using multivariate analysis. In patients who underwent HSCT from related donors, age ≥ 14 years at transplantation was risk factor of BSI. By contrast, history of immunosuppressive therapy with ATG, frequent blood transfusion before transplantation, graft failure and major or major+minor mismatch of ABO blood type were risk factors of BSI in patients who underwent HSCT from unrelated donors. Since the overall 5-year survival rate without BSI was over 90%, even in patients who were transplanted from an unrelated donor, control of BSI is very important for success of HSCT in patients with pediatric AA.