Cystic echinococcosis (CE), a neglected zoonotic disease, remains a significant public health challenge in low- and middle-income regions. This study systematically evaluates the global, regional, and national burden of CE from 1990 to 2021 and projects trends to 2036 using data from the Global Burden of Disease Study 2021. We analyzed age-standardized prevalence (ASPR), incidence (ASIR), mortality (ASMR), and disability-adjusted life years (ASDR) across 204 countries, stratified by Socio-demographic Index (SDI). Decomposition analysis assessed contributions of population aging, growth, and epidemiological changes. An autoregressive integrated moving average (ARIMA) model projected future disease burden. Globally, ASPR increased slightly from 7.37 to 7.69 per 100,000 (EAPC = 0.31%, 95% CI: 0.15%-0.47%) between 1990 and 2021, while ASMR declined sharply (EAPC = − 4.83%, 95% CI: -4.90%–4.76%). Low-SDI regions bore the highest burden (ASPR = 9.88 vs. 1.67 per 100,000 in high-SDI regions). Middle-aged populations (45–69 years) and females faced disproportionate risks. Projections indicate stable ASPR/ASIR but declining ASMR/ASDR by 2036. Regional disparities persisted, with Southern Latin America and Central Asia having the highest prevalence. Despite progress in mortality reduction, CE burden remains elevated in low-resource settings. Prioritizing interventions in low-SDI regions, adults aged 45–69 years, and women, alongside One Health strategies, is critical to narrowing inequities.