Cord blood transplantation (CBT) is a valuable donor source for patients without human leukocyte antigen (HLA)-matched donors. While CBT has a lower risk of graft-versus-host disease and requires less stringent histocompatibility, it is associated with a higher transplantation-related mortality (TRM) compared to other donor sources. We hypothesized that assessing the immunogenicity of mismatched HLA could reveal non-permissive mismatches contributing to increased TRM. We retrospectively analysed 1498 single-unit CBT cases from 2000 to 2018 across eight Japanese institutions, evaluating the immunogenicity of mismatched HLA using the PIRCHE algorithm to examine binding affinities of HLA-derived epitopes to donor or recipient HLA. Results indicated that Class I epitopes from mismatched recipient HLA-B were significantly associated with poor outcomes due to higher TRM and lower neutrophil engraftment, particularly when presented on matched HLA class I. Notably, epitopes from HLA-B exon 1 showed stronger prognostic significance, with HLA-B alleles carrying M-type leader peptides exhibiting higher affinity for these epitopes. Patients with a matched M-type HLA-B and Class I epitopes derived from mismatched HLA-B exon 1 had worse outcomes. These findings suggest that immunogenicity-informed donor selection could improve CBT outcomes.