Epstein-Barr virus (EBV) DNAemia and reactivation is a typical complication after allogeneic hematopoietic stem cell transplantation (HSCT). The degree of immunosuppression is closely linked to the risk of developing EBV DNAemia. An association of cyclosporine levels with EBV DNAemia has not been interrogated. Here, we analyzed cyclosporine levels in 58 patients after allogeneic HSCT. We discovered a wide range of cyclosporine trough level variation in the individual patient (median coefficient of variation [CV] 0.29, range 0.19-0.78). To overcome this high intra-individual variation in serum trough levels of cyclosporine, we calculated respective areas under the curve (AUC) and performed correlations with EBV DNAemia in 28 stem cell recipients at increased risk for EBV DNAemia. This resulted in a significant association of high cyclosporine AUC (> 6000 ng/mL × days) with EBV DNAemia after day 30 (relative risk [RR] 6.067, 95% confidence interval [CI] 1.107-33.238, p = 0.038). Conversely, mean cyclosporine values (threshold 200 ng/mL) between days 0 and 30 were not found to correlate with EBV DNAemia after day 30. Furthermore, CD3 + CD8 + graft content was inversely correlated with EBV DNAemia after day 30. These findings might establish a clinical role for the AUC of cyclosporine.