Introduction : Hematopoietic stem cell transplantation (HSCT) has been applied as the curative treatment for rare pediatric non-malignant diseases. We evaluate the outcome of 41 patients treated with HSCT. Method : We performed a retrospective analysis of 43 HSCT performed in 41 patients with rare non-malignant diseases between May 2002 and May 2017. Reduced intensity conditioning regimens were applied from 2011. In haploidentical hematopoietic stem cell transplantation (HHCT), a combination of fludarabine, cyclophosphamide and ATG was mostly used before 2016, while treosulfan based combination was uniformly used since 2016. Grafts for HHCT were manipulated by ex vivo CD3 or αβ+ T-cell depletion. Results : This study included 14 patients with congenital immunodeficiency, 13 with congenital bone marrow failure syndrome, 5 with degenerative metabolic disease, 2 with disease of RBC and 7 with familial hemophagocytic lymphohistiocytosis. Nine patients received grafts from matched familial donor, 22 from matched unrelated donor, and 10 from haploidentical family donor. The median age at HSCT was 2.5 years. Thirty eight of 41 patients reached neutrophil engraftment, with a median of 11 days without significant difference between donor types ( P=0.355). Graft failure occurred in 4 patients (3 primary, 1 secondary); 3 patients including 2 patients who underwent second HHCT died and 1 patient is alive without further HSCT. Grade II-IV acute GVHD occurred in 12 patients, while chronic GVHD occurred in 4. At a median follow up 56 months, the 5-year overall survival (OS) and event free survival (EFS) was 85.4% and 82.9%, respectively. Total 6 patients died, and 5 patients died of transplant-related events. There was no statistical difference in OS and EFS among HSCT from 3 different donor types ( P=0.367). Patients who received HSCT at younger age (500 days) had a worse outcome compared to the older age group ( P=0.038). By disease categories, patients with congenital immunodeficiency tended to have a lower OS ( P=0.074). Conclusion : In this study of pediatric rare non-malignant diseases, outcomes of HHCT were comparable to HSCT from other donor types, with no statistically significant difference in neutrophil engraftment, OS and EFS. The improvement of this treatment will offer a better chance of cure in patients with pediatric rare non-malignant diseases.