Background Pediatric brain and central nervous system (CNS) cancers are the second most common childhood malignancy, yet global burden trends and disparities remain understudied. Methods Using Global Burden of Disease (GBD) 1990–2021 data, we analyzed incidence, mortality, prevalence, and disability-adjusted life years (DALYs) in children aged 0–14 years across 204 countries. Joinpoint regression identified temporal inflection points, decomposition analysis quantified DALY drivers (population growth, aging, epidemiology), and Bayesian Age-Period-Cohort models projected burdens to 2036. Results Global incidence declined by 0.54% annually (1990–2021), with similar reductions in DALYs (-1.49%/year) and mortality (-1.46%/year). High-SDI regions achieved burden reductions through early diagnosis and advanced therapies, while low-SDI regions (e.g., sub-Saharan Africa) experienced rising burdens due to healthcare resource limitations. Decomposition analysis revealed epidemiological improvements drove DALY declines in high-SDI areas, whereas population growth increased burdens in low-SDI settings. Projections indicate persistent global declines by 2036, but regional disparities may widen without targeted interventions. Conclusion Strengthening diagnostic capacity and equitable access to therapies in low-resource settings is critical to reducing global disparities. This study provides evidence to guide policy reforms for pediatric CNS cancer control.