Paroxysmal nocturnal hemoglobinuria (PNH) is a rare clonal disease of hematopoietic stem cell characterized by complement mediated intravascular hemolysis. There are different treatment modalities available for PNH, such as supportive care, eculizumab, and hematopoietic stem cell transplantation (HSCT); only the last one has a potential curative role. This study reported the outcome of HSCT transplanted PNH patients. Thirteen PNH patients between 2002 and 2014 participated in this study. All had full-matched sibling donors, and the conditioning regimen was Bu/Cy (busulfan plus cyclophosphamide), and the source of stem cells was peripheral blood of the donors. Mean age at transplant was 27.46 years, and mean time to transplant was 41.30 months. Three were female and 10 were male. Three patients died at the end of follow-up time, and the cause of death was graft versus host disease (GVHD) for all 3 cases. Survival analysis showed a 5-year and a 13-year survival rate of 74.07% and a significant relationship between a positive history of thrombosis and a higher mortality rate. HSCT has curative role in management of PNH with an acceptable survival rate and therefore can be considered as an acceptable choice for selected cases.