Objective To investigate the efficacy of allogeneic hematopoietic stem cell transplantation (HSCT) in the treatment of children with dyskeratosis congenita (DKC), and to provide a basis for exploring the optimal transplantation program. Methods The clinical data of 3 children with DKC treated by HSCT in our hospital from June 2019 to June 2022 were retrospectively analyzed and the related literatures were reviewed. Results Three patients all underwent HSCT with a fludarabine-based reduced-intensity conditioning (RIC) regimen. The median count of mononuclear cells (MNC) and CD34⁺ cells was 13.7(8.3-17.3)×10⁸/kg and 8.2(6.3-13.1)×10⁶/kg respectively. A combination of methotrexate, cyclosporin A and mycophenolate mofetil was used to prevent graft-versus-host disease (GVHD). All 3 patients were able to tolerate the HSCT pretreatment. The median time of neutrophil implantation was 11(10-11) days, and the median time of platelet implantation was 11(10-13) days, and no primary implantation failure occurred. Two patients developed acute GVHD of different severity, 1 developed chronic GVHD, and 1 developed reversible posterior leukoencephalopathy syndrome (RPLS) after transplantation. The follow-up was completed in January 2023 and the median follow-up time was 19(11-42) months. All 3 patients survived, and 1 had chronic GVHD. At present, all 3 children were free from blood transfusion, and no DKC-related gene mutation was detected in blood cells after transplantation. The growth and development of the patients was similar to that of normal children of the same age, and no combined solid tumor has been found. Conclusions The pretreatment regimen of " Flu+low-dose cyclophosphamide (CTX) + anti-thymocyte globulin (ATG)" for HSCT treatment in DKC patients was tolerable, and no primary implantation failure occurred. GVHD is still the main factor affecting the survival of children, and it is necessary to explore the clinical study of individualized treatment for DKC.