(1) Background: Post-transplant lymphoproliferative disorder (PTLD) is a hematological disease and occurs because of immunosuppression after organ transplantation. Only a few studies have reported PTLD in the nasopharynx. In most cases, PTLD developed after solid organ transplantation, and cases of PTLD after bone marrow transplantation, are uncommon. (2) Case presentation: We report the case of a 40-year-old woman with myelodysplastic disorder who underwent hematopoietic stem cell transplantation (HSCT). After 3 months, she developed low-grade fever, progressive nasal obstruction, and bloody rhinorrhea. Endoscopy revealed a mass completely occupying the nasopharynx. A polymorphic PTLD was diagnosed on the basis of histopathological examination results. Reduction in immunosuppression and low-dose radiotherapy were prescribed for treatment. After a 3-year follow-up, no recurrence of PTLD or myelodysplastic disorder was detected. (3) Conclusions: While nasopharyngeal PTLD is rare, a routine examination of the nasopharynx should be considered in the post-transplant follow-up of patients for early detection and treatment of PTLD.