OBJECTIVES: To estimate the global burden of malaria and neglected tropical diseases (NTDs) in children and adolescents aged 0-19 years and to analyse trends to inform public health and policy decisions. DESIGN: Population-based, cross-sectional study. SETTING: Global analysis across 204 countries and territories. PARTICIPANTS: Children and adolescents aged 0-19 years with malaria and NTDs, stratified by age, gender and location from 1990 to 2019. MAIN OUTCOME MEASURES: Yearly incidence, prevalence, and disability-adjusted life years (DALYs) for malaria and NTDs, age-standardised incidence rates (ASIRs) and age-standardised DALY rates (ASDRs). RESULTS: The global burden of malaria and NTDs among children and adolescents aged 0-19 years remains substantial. In 2019, 195.6 million cases of malaria and NTDs were recorded globally, resulting in 43.9 million (95% Uncertainty Interval (UI): 25.0-70.4 million) DALYs. The incidence rate increased until 2005 and then declined. Sub-Saharan Africa had the highest ASDR, while high-income regions had the lowest. Significant ASDR reductions occurred in Andean Latin America and South Asia. The burden was highest in low-Socio-Demographic Index (SDI) regions, with malaria accounting for over 93% of DALYs among children under five. Females had slightly higher incidence rates, while DALYs were evenly distributed between genders. There was an inverse association observed between SDI and ASDRs. CONCLUSIONS: Malaria and NTDs continue to disproportionately affect children and adolescents in low-SDI regions, especially sub-Saharan Africa. Sustaining gains while accelerating control efforts is the key to successful control progress and ambiguous elimination goals for both malaria and NTDs.