Post‐transplantation lymphoproliferative disorders (PTLD) are life‐threatening complications of organ transplantation caused by EBV infection and the use of chronic immunosuppression. While T‐cell impairment is known to play a critical role in the immunopathogenesis of EBV complications post‐transplantation, the role of NK cells is still under investigation. Here, we have characterized NK‐cell phenotype and function in peripheral blood from asymptomatic pediatric thoracic transplant patients, patients with PTLD, and healthy controls. Overall, asymptomatic pediatric solid organ transplant (Tx) patients presented significant expansion of the CD56^brightCD16^± subset and displayed effective NK‐cell function, while PTLD patients accumulated CD56^dimCD16⁻ and CD56⁻CD16⁺ NK‐cell subsets. In addition, NK cells from PTLD patients down‐regulated NKp46 and NKG2D, and significantly up‐regulated PD‐1. These phenotypic changes were associated with NK functional impairment, resembling cellular exhaustion. Disrupting PD‐1 inhibitory pathway improved IFN‐γ release, but did not enhance cytotoxicity in PTLD patients, suggesting that these defects were partially PD‐1 independent. Our results indicate the important role of NK cells during EBV surveillance post‐transplantation, with implications for the immunopathogenesis of EBV complications, and suggest that monitoring NK cells in transplant patients may hold clinical value.