Worldwide, diarrhea is the second most common cause of death and morbidity among under -five years' children. In sub-saran Africa, access to water, sanitation, and hygiene are very scanty and the burden of diarrhea diseases is countless relative to the rest of the world. Prior studies conducted in East Africa vary in design, sample size, and other data collection tools. Through those studies, it is hard to make regional comparisons. Combining datasets that are studied on similar people and having common variable identified enhances statistical power due to the large sample size, advance the ability to compare outcomes, and create the opportunity to develop new indicators. Hence, this study aimed to assess the prevalence and associated factors of diarrhea among under five years' children using the most recent national representative Demographic and Health Surveys from 12 East African countries. The information generated from this pooled datasets will give good insight into the sub-regional prevalence of diarrhea. This study utilized secondary data from 12 East African countries' most recent demographic health survey. Variables were extracted and appended together to assess the pooled prevalence of diarrhea and associated factors. A total of 90,263 under-five years of age children were encompassed in this study. STATA version was used to cross-tabulate and fit the models. To account for the hierarchical nature of the demographic health survey, multilevel logistic regression was calibrated. BIC, AIC, deviance, and LLR were used as Model comparison parameters. Variables with a p-value of <0.2 were considered for multivariable analysis. Adjusted odds ratio with 95% CI and p-value <0.05 were used to declare statistical significances of factors. The pooled prevalence of diarrhea in under five years children was 14.28% [95%CI; 14.06%, 14.51%]. Being child whose mother age is 15-24 years [AOR = 1.41, 95% CI; 1.33, 1.49], 25-34 years[AOR = 1.17, 95%CI; 1.10, 1.23], being 7-12 months child [AOR = 3.10, 95%CI; 2.86, 3.35], being 12-24 months child [AOR = 2.56, 95%CI; 2.38, 3.75], being 25-59 months child [AOR = 0.88, 95%CI; 0.82, 0.95], being child from poor household [AOR = 1.16, 95%CI; 1.09, 1.23], delayed breast feeding initiation (initiated after an hour of birth) [AOR = 1.15, 95%CI; 1.10, 1.20], and being a child from community with low educational status [AOR = 1.10, 95%CI; 1.03, 1.18] were factors associated with diarrheal diseases. The pooled prevalence of diarrhea among under five years of children in East African countries is high. Maternal age, child's age, wealth status of the household, the timing of breast feeding initiation, sex of the child, community level of educational status, working status of the mother, and the number of under five children were factors that were associated with diarrheal diseases. Scaling up of maternal and child health services by government and other concerned bodies should consider those economically marginalized communities. Additionally, awareness should be created for those uneducated mothers concerning the nature of childhood diarrhea.