Core-binding factor acute myeloid leukemia (CBF-AML) generally has a favorable prognosis, with allogeneic hematopoietic stem cell transplantation (allo-SCT) recommended for relapsed/ refractory (R/R) cases achieving second complete remission (CR). However, clinical outcomes remain suboptimal for patients who relapse or fail to achieve CR following induction chemotherapy. Allo-SCT in non-CR is a potential strategy for such patients, though supporting evidence in CBF-AML is limited. To assess outcomes and prognostic factors of allo-SCT in R/R CBF-AML with active disease, we conducted a retrospective analysis of 610 patients with CBF-AML in non-CR undergoing allo-SCT from 2010 to 2021 across 174 centers within the European Society for Blood and Marrow Transplantation. Graft sources included matched sibling (MSD, n = 151), unrelated (UD, n = 368), and haploidentical donors (Haplo, n = 91). Among patients, 124 had inv(16), and 486 had t(8;21). Two-year overall survival (OS) and leukemia-free survival (LFS) were 53.6% and 42.7%, respectively. Haplo-SCT showed inferior OS compared to MSD (HR 1.79, p = 0.003) and UD (HR 1.64, p = 0.004) and reduced chronic graft-versus-host disease. Patients with t(8;21) exhibited higher relapse incidence (HR 2.04, p = 0.002) and poorer survival outcomes than those with inv(16). These findings confirm the therapeutic role of allo-SCT in R/R CBF-AML in non-CR, supporting its favorable risk profile.