Post-transplant lymphoproliferative disorder (PTLD) is a rare, but severe Epstein-Barr virus (EPV)-driven disorder that manifest after hematopoietic stem cell transplantation (HSCT) or solid organ transplantation (SOT). This heterogenous disease may manifest as localized or disseminated, and clinical presentation may differ significantly. It may be difficult to early diagnose PTLD, as is may be misdiagnosed as infection or graft rejection. The majority of EBV-PTLD typically occurs within four months following HSCT, and almost all cases present within the first year. EBV-PTLD that manifests > 5 years is considered an exceedingly rare occurrence. We describe a case of 66-year-old male, who was diagnosed with high-risk chronic lymphocytic leukemia (CLL). He underwent allogeneic HSCT from HLA-identical sister, and subsequently developed acute followed by chronic graft-versus-host disease, for which he was long-term treated with immunosuppressants. At 6 years following HSCT, the patient presented with life-threatening perforation of gut. Histological evaluation revealed diffuse large B cell lymphoma. Serum sample test showed positive EBV DNA and diagnosis of probable EBV-PTLD was done. After the treatment with rituximab, along with the reduction of immunosuppression, the patient achieved complete remission. Late onset EBV-PTLD after HSCT is extremely uncommon, and hardly described in literature.