The cytogenetic risk category retains a pivotal role in the prediction of prognosis in acute myeloid leukemia (AML) patients undergoing hematopoietic stem cell transplantation (HSCT), however, its impact on secondary AML (sAML) is less established. We assessed whether the ELN 2022 cytogenetic risk score predicts outcomes in sAML patients in remission undergoing HSCT from HLA-matched donors performed between 2010 and 2022. Among 1119 patients, 829 had intermediate and 284 had adverse cytogenetics (6 with favorable risk were excluded). Engraftment rates was 72.4% vs. 99.5%. Acute graft-versus-host disease (GVHD) incidence did not differ, but 2-years all grades and extensive chronic GVHD were higher in the intermediate vs. adverse cytogenetics risk groups, hazard ratio (HR) = 0.72; p = 0.034 and HR = 0.58; p = 0.027, respectively. Two-year non-relapse mortality (NRM) was similar. All other HSCT outcomes were inferior in the adverse risk vs. intermediate-risk patients: The HR for 2-year relapse incidence (RI) was 2.48 (95% CI 1.95-3.15, p < 0.001). The HRs for 2-year leukemia-free survival (LFS), overall survival (OS), and GVHD-free/relapse-free survival (GRFS) were 1.62 (95% CI 1.34-1.95, p < 0.001), 1.59 (95% CI 1.3-1.93, p < 0.001) and 1.38 (95% CI 1.15-1.65, p < 0.001), respectively. We conclude that cytogenetic risk score predicts HSCT outcomes in sAML patients.