Hematopoietic stem cell transplantation (HSCT) is the only curative treatment for bone marrow failure (BMF) in patients with Fanconi anemia (FA). We retrospectively analyzed the records of patients with FA who underwent HSCT with a radiation-free, reduced-intensity conditioning regimen (fludarabine, cyclophosphamide, and antithymocyte globulin) along with an unmanipulated graft infusion between 2004 and 2018. A total of 44 patients underwent HSCT during the study period. Median age at transplantation was 121 months. Regarding the donor source, 22 transplants (50%) were collected from matched related donors (MRDs), and 22 transplants (50%) were collected from alternative donors (ADs). The median infused CD34+ cell dose was 4.7 × 106/kg (range, 0.8 to 23) in bone marrow or peripheral blood stem cell recipients and 1.2 × 105/kg (range, 1.1 to 3.6) in umbilical cord blood recipients. All but 2 patients achieved primary neutrophil engraftment (95%). In a median follow-up of 36 months (range, 1 to 159), 3-year overall survival was 70.5% in the entire group and 91% in the MRD recipients. Primary causes of death were infections (n = 5), acute grade 3 to 4 graft-versus-host disease (n = 4), and hemorrhagic cystitis (n = 3). All surviving patients have full (n = 29) and acceptable mixed (n = 2) donor chimerism and good clinical status. Our results showed an excellent outcome with unmanipulated grafts using a fludarabine-based, radiation-free preparative regimen for MRD recipients. Even though primary neutrophil engraftment rates were good in AD recipients, intervening complications increased mortality in these patients. In clinics where T cell depletion is not feasible, more effort is warranted to improve outcomes for AD recipients.