Objective To evaluate the diagnostic value of plasma Epstein-Barr virus (EBV) DNA load and the duration of EBV DNAemia for post-transplant lymphoproliferative disorders (PTLD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in children. Methods Clinical data of children who underwent allo-HSCT at Shenzhen Children's Hospital from January 2016 to December 2023 and had plasma EBV-DNA positivity after transplantation were retrospectively analyzed. According to the occurrence of PTLD, patients were divided into a PTLD group (n=53) and a non-PTLD group (n=376). Results A total of 429 children were included; 53 (12.4%) developed PTLD, with a median time to PTLD diagnosis of 85 days post‑transplant. Peak plasma EBV-DNA load and the duration of EBV DNAemia were both significantly higher in the PTLD group than in the non-PTLD group (both P<0.001). Receiver operating characteristic curve analysis for predicting PTLD showed that using 2 250 copies/mL as the cut-off for plasma EBV-DNA load yielded the highest Youden index (sensitivity 0.811; specificity 0.699), while using 12.5 days as the cut-off for the duration of EBV DNAemia yielded the highest Youden index (sensitivity 0.868; specificity 0.870). Conclusions Dynamic monitoring of plasma EBV-DNA load and the duration of EBV DNAemia helps predict the occurrence of PTLD and facilitates early intervention in children after allo-HSCT.