The use of post-transplant cyclophosphamide (PTCy) for graft-versus-host disease (GVHD) prophylaxis in severe aplastic anemia (SAA) remains understudied, particularly beyond haploidentical transplants. We analyzed outcomes of SAA patients who underwent stem cell transplantation (SCT) with PTCy from haploidentical donors (n = 209), HLA-matched sibling donors (MSD, n = 70), and unrelated donors (UD, n = 69) using EBMT data from 2010 to 2022. Median age was 22 years, and median time to transplantation was 8.6 months. For haploidentical, MSD, and UD cohorts, the 100-day cumulative incidence of grade II-IV acute GVHD was 19%, 11%, and 14% (p = 0.15), while grade III-IV was 6%, 3%, and 2% (p = 0.1). Two-year chronic and extensive chronic GVHD were 14%, 13%, and 14% (p = 0.1) and 5%, 6%, and 2% (p = 0.5), respectively. Non-relapse mortality at two years was 24% for haploidentical, 7% for MSD, and 10% for UD (p = 0.003). Two-year overall survival (OS) and GVHD- and relapse-free survival were 66% and 54% for haploidentical, 92% and 70% for MSD, and 81% and 66% for UD (p < 0.001, p = 0.06). In multivariable analysis, MSD and UD were associated with superior OS and GRFS compared to haploidentical. PTCy is safe and effective in SAA patients, though haploidentical SCT had higher NRM, leading to lower survival.