Background: Despite widespread vaccination, pertussis persists as a critical global public health threat, particularly for individuals under 20 years old. This study aimed to comprehensively assess the global burden of pertussis in this population, with a specific focus on disparities related to age, sex, location, and socioeconomic development. Methods: We utilized data from the Global Burden of Disease (GBD) study 2021 to quantify the burden of pertussis including incidence, mortality, disability-adjusted life years (DALYs) among individuals under 20 years old across 204 countries and territories from 1990 to 2021. Burden estimates were stratified by age, sex, location, and socio-demographic index (SDI). Temporal trends were assessed using estimated annual percentage change (EAPC), and the association between burden metrics and SDI was evaluated via smoothing spline models and Spearman’s correlation analysis. Results: From 1990 to 2021, the global incidence of pertussis in individuals under 20 years old decreased by 77.7%. Similarly, deaths and DALYs due to pertussis declined by 80.3%. In 2021, low-SDI regions reported the highest number of pertussis cases, deaths, and DALYs, whereas high-SDI regions had the lowest. Geographically, South Asia had the highest case count, and Western Sub-Saharan Africa led in deaths and DALYs. Infants had the highest incidence, mortality, and DALY rates. Gender disparities were observed, with females generally having higher rates than males, except in Eastern Sub-Saharan Africa. A negative correlation was noted between SDI and pertussis burden. Conclusions: Our study provides valuable insights into the global pertussis burden among individuals under 20 years old. Despite overall improvements, significant variations exist. Our findings emphasize the need for sustained and improved vaccination strategies such as maternal immunization, improved coverage and timeliness, and better healthcare access, to further address these inequalities.