Allogeneic haematopoietic stem cell transplantation (allo‐HSCT) is the only curative therapy for adult T‐cell leukaemia/lymphoma (ATL). Specific HLAs are associated with outcomes of immunotherapy and allo‐HSCT. We hypothesised that individual HLAs would affect the clinical outcomes of ATL patients after allo‐HSCT. Using data from a Japanese registry, we retrospectively analysed 829 patients with ATL who received transplants from HLA‐identical sibling donors or HLA‐A, ‐B, ‐C or ‐DRB1 allele‐matched unrelated donors between 1996 and 2015. We evaluated the overall mortality risk of HLA‐A, ‐B and ‐DR antigens with frequencies exceeding 3%. Outcomes were compared between transplants with or without specific HLA antigens. Of the 25 HLAs, two candidates were identified but showed no statistically significant differences by multiple comparison. HLA‐B62 was associated with a lower risk of mortality (hazard ratio [HR], 0.68; 95% confidence interval [CI]: 0.51–0.90; p = 0.008), whereas HLA‐B60 was associated with a higher risk of mortality (HR, 1.64; 95% CI: 1.19–2.27; p = 0.003). In addition, HLA‐B62 was associated with a lower risk of transplant‐related mortality (TRM) (HR, 0.52; 95% CI: 0.32–0.85, p = 0.009), whereas HLA‐B60 was associated with a higher risk of grades III–IV acute graft‐versus‐host disease (HR, 2.63; 95% CI: 1.62–4.27; p < 0.001). Neither HLA influenced relapse. The higher risk of acute GVHD in HLA‐B60‐positive patients and the lower risk of TRM in HLA‐B62‐positive patients were consistent with previously obtained results from patients with other haematological malignancies. Consideration of HLA in ATL patients may help to predict risk and outcomes after allo‐HSCT.