Context Hematopoietic stem cell transplantation (HSCT) became an integral component of the treatment of various pediatric malignancies. Post-transplant central nervous system complications (CNSC) are major contributors to morbidities in transplanted patients. Objective To describe the patterns of CNSC after HSCT in pediatric oncology patients using brain imaging. Design This retrospective study included pediatric patients transplanted between 2011 and 2019. Setting Cases were treated at the Children’s Cancer Hospital Egypt (CCHE-57357), which is a specialized center for pediatric oncology. Patients or Other Participants The study included pediatric cases who had undergone allogeneic- or autologous-HSCT. Interventions Computed tomography (CT) and/or magnetic resonance imaging (MRI) studies were evaluated for the detection and characterization of CNSC. Imaging was done following any neurological symptoms post-transplant. Brain structural abnormalities were classified as cerebrovascular complications (intra-parenchymal hemorrhage and venous thrombosis), infection, disease recurrence, atrophy, and treatment-related toxicities (posterior reversible encephalopathy syndrome [PRES] and leukoencephalopathy). Main Outcome Measures To describe the pattern of CNSC post-HSCT in pediatric oncology patients using CT and/or MRI. Results A total of 525 cases were included, of whom 311 and 214 had undergone autologous-HSCT and allogeneic-HSCT, respectively. Median follow-up for survivors was 48 months (range: 6–109 months). Hematological malignancies constituted 58% of cases. The median age was 6.5 years (range: 0.9–25 years). Sixty-eight cases (13%) presented cumulatively with 77 clinical episodes of neurological complications. The cumulative frequency of CNSC at 100 days was 5.3%. A higher incidence was observed in allogeneic-HSCT (15.9 %) compared to autologous-HSCT (11%). The most common CNSC was disease recurrence in 28/77 (36.4%), with 89% occurrence after autologous-HSCT, followed by PRES in 17/77 (22%) episodes. Females were 4.2 times as susceptible to developing PRES as males (p Conclusion The frequency of post-transplant CNSC is higher in allogeneic-HSCT compared to autologous-HSCT. The pattern of CNSC differs according to the time interval post-HSCT. Expert imaging interpretation is needed for early detection and proper management of CNSC post-HSCT.