Human leukocyte antigen (HLA)‐haploidentical hematopoietic stem cell transplantation (haplo‐HSCT) is an effective alternative to HLA‐matched transplantation. However, Epstein‐Barr virus (EBV) infection causes morbidity and mortality in patients undergoing haplo‐HSCT. Here, we retrospectively evaluated the incidence and risk factors of EBV‐DNAemia and EBV‐associated diseases in 131 patients who underwent haplo‐HSCT. Patients were classified into the no EBV infection groups, EBV‐DNAemia group and EBV‐associated disease group. Cumulative incidences of acute graft‐vs‐host disease, EBV infections, overall survival (OS), and relapse were analyzed. The cumulative incidences of EBV‐DNAemia and EBV‐associated disease were 26.9% and 33.3%, respectively. In multivariate analysis, cytomegalovirus (CMV)‐DNAemia was confirmed as an independent risk factor associated with EBV‐DNAemia and EBV‐associated disease. Patients with EBV‐associated disease had higher transplant‐related mortality (TRM) rates and lower OS rates, but similar relapse rates. Overall, these findings demonstrated the cumulative incidences of EBV‐DNAemia and EBV‐associated disease and identified correlations of EBV infection with TRM, relapse, and OS. Additionally, CMV‐DNAemia was a risk factor for EBV‐DNAemia and EBV‐associated disease.