Epstein-Barr virus- (EBV-) induced posttransplantation lymphoproliferative disease (PTLD) is a life-threatening complication following allogeneic stem cell transplantation. The main risk factor is anti-thymocyte globulin (ATG). Patients who fail first-line treatment with rituximab have a poor prognosis. Though adoptive transfer of EBV-specific T cells is a potentially effective option, it is not readily available. In this case report, the patient developed PTLD following transplantation for aplastic anemia using ATG as part of the conditioning. He failed rituximab treatment and developed graft failure. We were aware that the stem cell donor had a recent EBV infection prior to transplantation, whereas the patient most likely was EBV negative before transplant. We describe our strategy to meet the patient’s urgent need for EBV-specific T cells, as well as new hematopoietic stem cells. The same donor was used for a second transplant, using peripheral blood stem cells. The conditioning used was thiotepa/busulfan/fludarabin with a single dose of cyclophosphamide after transplant as graft-versus-host disease (GVHD) prophylaxis. The EBV DNA levels fell when conditioning was started, and have been undetectable since day +15 and remained so till 18 months after transplantation. The patient is doing well. This case reports successful use of cyclophosphamide after transplantation as GVHD prophylaxis, preserving virus-specific immunity.