Objective To investigate the clinical feature of central nervous system post-transplant lymphoproliferative disorder (CNS-PTLD) after allogeneic hematopoietic stem cell transplantation (allo-HSCT) in children. Methods Firstly, we retrospectively analyzed the clinical data of one case after transplantation, then summarized relevant literature. Results The child, a 13-year-old male, was diagnosed with acute myeloid leukemia M5 (positive for TLS-ERG fusion gene), achieved complete remission with remission chemotherapy, turned negative for TLS-ERG, and then turned positive for TLS-ERG after 2 courses of MAE regimen and high-dose cytarabine based regimen, showed molecular biological relapse and was eligible for transplantation, so allo-HSCT was performed (paternal donor, HLA 5/10). Fever developed at +162d after transplantation, with a higher fever peak at +170d than before, and apathy, lethargy, headache and vomiting. In combination with cranial CT and enhanced MRI findings, cerebrospinal fluid EBV DNA amount (14903 copies/mL), and cerebrospinal fluid second-generation sequencing results (human gamma herpesvirus type 4 (EBV) DNA sequences up to 13717), primary central nervous system lymphoproliferative disorder (PCNS-PTL) was considered, and ganciclovir antiviral and rituximab treatment was given. The child’s malaise, nausea and drowsiness improved significantly on +179d, but a sudden cerebral hemorrhage with brain herniation occurred on +186d, and he died in resuscitation. Conclusion The incidence of PCNS-PTLD is very low, and it is difficult to diagnose and treat. For patients with central nervous system symptoms after transplantation, early diagnosis and timely treatment are necessary.