Abstract Background In 2017, an estimated 5.3 million under-five children died annually in Sub-Saharan African countries, more than half of those deaths occurred in East Africa. Though East African countries share the huge burden of global under-five mortality, there is limited evidence on the incidence and predictors of under-five mortality. Therefore, this study investigated the incidence and predictors of under-five mortality in East Africa. Methods A community-based cross-sectional study was done based on the Demographic and Health Survey (DHS) data of 12 East African countries conducted from 2008 to 2019. A total weighted sample of 138,803 live births within 5 years preceding the survey were included for analysis. The Kaplan-Meier curve and Log-rank test were done to assess the children’s survival experience across variable categories. The Global Schoenfeld residual test was employed for checking Proportional Hazard (PH) assumptions and it was violated ( p -value< 0.05). Considering the hierarchical nature of DHS data, multilevel parametric survival models were fitted. Model comparison was made by AIC, deviance, and shape of the hazard function. Variables with a p -value of less than 0.2 in the bi-variable analysis were considered for the multivariable analysis. In the multilevel Weibull regression analysis, the Adjusted Hazard Ratio (AHR) with 95% Confidence Interval (CI) was reported to declare the significant predictors of under-five mortality. Results Under-five mortality rate in East Africa was 51.318 (95% CI: 51.311, 51.323) per 1000 live births. Babies born to mothers attained secondary education and above (AHR = 0.83, 95% CI: 0.75, 0.91), being 2nd - 4th birth order (AHR = 0.62, 95% CI: 0.56, 0.67), ≥ 5th birth order (AHR = 0.68, 95% CI: 0.61, 0.76), health facility delivery (AHR = 0.87, 95% CI: 0.82, 0.93), 1–3 ANC visit (AHR = 0.61, 95% CI: 0.54, 0.68), births interval of 24–48 months (AHR = 0.53, 95% CI: 0.50, 0.57), wanted pregnancy (AHR = 0.72, 95% CI: 0.68, 0.76), middle wealth status (AHR = 0.90, 95% CI: 0.83, 0.97), and richest wealth status (AHR = 0.81, 95% CI:0.73, 0.90) were significantly associated with lower hazards of under-five mortality. Whereas, advanced maternal age (≥35 years) (AHR = 1.13, 95% CI: 1.04, 1.24),, babies born to household who did not have media exposure (AHR = 1.13, 95% CI: 1.07, 1.20), twin births (AHR = 3.81, 95% CI: 3.52, 4.12), being male child (AHR = 1.27, 95%CI: 1.21, 1.33), small birth size at birth (AHR = 1.73, 95% CI: 1.63, 1.84), and large size at birth (AHR = 1.11, 95% CI: 1.04, 1.11) were significantly associated with higher hazards of under-five mortality. Conclusion Under-five mortality is a major public health concern in East African countries. Health facility delivery, ANC visit, higher wealth status, adequate birth spacing, wanted pregnancy, and maternal education were significantly correlated with a lower risk of under-5 mortality. Whereas, higher birth order, small or large size at birth, male birth, twin birth, advanced maternal age and mothers who didn’t have media exposure were significantly correlated with a higher risk of under-five mortality. This study highlights that public health programs should enhance health facility delivery, ANC visit, media exposure, maternal education, and adequate birth spacing to decrease the incidence of under-five mortality in East Africa.