Background Childhood undernutrition is the leading cause of under-five mortality and morbidity in the world particularly in East African countries. Although there are studies on child undernutrition in different East African countries, our search of the literature revealed that there is limited evidence of a pooled analysis of these studies. Therefore, this study aimed to investigate the pooled prevalence and associated factors of chronic undernutrition (i.e. stunting) among under-five children in East Africa. Methods A pooled analysis of the Demographic and Health Surveys (DHSs) in 12 East African countries was conducted. A total weighted sample of 79744 under-five children was included in the study. Mixed-effect logistic regression analysis was used to identify significant factors associated with chronic undernutrition since the DHS data has a hierarchical structure. The intra-class correlation coefficient (ICC), Median Odds Ratio (MOR), Likelihood Ratio (LR)-test, and deviance was used for model comparison. Variables with p-value <0.2 in the bivariable mixed-effect logistic regression analysis were considered for the multivariable analysis. In the multivariable multilevel analysis model, the Adjusted Odds Ratio (AOR) with the 95% Confidence Interval (CI) were reported for significant factors. Results The pooled prevalence of chronic undernutrition among underfive children in East Africa was 33.3% (95% CI: 32.9%, 35.6%) ranging from 21.9% in Kenya to 53% in Burundi. Children whose mothers lived in rural area (AOR = 1.11, 95% CI: 1.06, 1.16), born to mother who had no formal education (AOR = 1.42, 95% CI: 1.34, 1.50) and primary education (AOR = 1.37, 95% CI: 1.31, 1.44), being in poor household (AOR = 1.66, 95% CI: 1.58, 1.74), and middle household (AOR = 1.42, 95% CI: 1.35, 1.49), child aged 36–48 months (AOR = 1.09, 95% CI: 1.04, 1.14), being male (AOR = 1.19, 95% CI: 1.15, 1.23), 2^nd - 4^th birth order (AOR = 1.08, 95% CI: 1.03, 1.13), and above 4^th 1.27 (AOR = 1.27, 95% CI: 1.19, 1.35), home delivery 1.09 (AOR = 1.09, 95% CI: 1.05, 1.13), small size at birth (AOR = 1.35, 95% CI: 1.29, 1.40) and being multiple births (AOR = 1.98, 95% CI: 1.81, 2.17) were associated with increased odds of stunting. While, antenatal care visit (AOR = 0.89, 95% CI: 0.86, 0.93), mothers aged 25–34 (AOR = 0.83, 95% CI: 0.79, 0.86) and ≥ 35 years (AOR = 0.76, 95% CI: 0.72, 0.81), large size at birth (AOR = 0.85, 95% CI: 0.81, 0.88), and family size >8 (AOR = 0.92, 95% CI: 0.87, 0.98) were associated with decreased odds of stunting. Conclusion The study revealed that stunting among under-five children remains a major public health problem in East Africa. Therefore, to improve child nutrition status the governmental and non-governmental organizations should design public health interventions targeting rural residents, and the poorest households. Furthermore, enhancing health facility delivery, ANC visit, and maternal health education is vital for reducing child chronic undernutrition.