Introduction Diarrhea is the leading cause of illness and death among under-five children in low and middle income countries. Through the provision of zinc supplements has been shown to reduce the severity and duration of diarrhea, as well as the risk of mortality, the use of zinc for the treatment of diarrhea is still very low in low-income countries. Therefore, this study was conducted to determine the prevalence and associated factors of zinc utilization among under-five children with diarrhea in East Africa. Methods A secondary data analysis of the recent Demographic and Health Surveys (DHS) of East African countries were used to determine the prevalence and associated factors of zinc utilization among under-five children with diarrhea in East Africa. A total weighted samples of 16,875 under-five children with diarrhea were included in the study. A generalized linear mixed model (using Poisson regression with robust error variance) was used. Prevalence Ratios (PR) with their 95% confidence interval (CI) were calculated for those variables included in the final model. Results The overall prevalence of zinc utilization among under-five children with diarrhea in this study was 21.54% (95% CI = 20.92–22.16). Of East African countries, Uganda had the highest prevalence of zinc utilization (40.51%) whereas Comoros had the lowest (0.44%). Maternal primary education (Adjusted Prevalence Ratio(aPR) = 1.29, 95% CI: 1.16–1.44), secondary education (aPR = 1.36, 95% CI = 1.19–1.55) and higher education (aPR = 1.91, 95% CI = 1.52–2.40), high community women education (aPR = 1.12, 95% CI = 1.02–1.24), high wealth index (aPR = 1.12, 95% CI = 1.01–1.24), high community media exposure (aPR = 1.17, 95% CI = 1.06–1.29) were associated with a higher prevalence of zinc utilization. Conclusion The prevalence of zinc utilization among under-five children was found to be low in East Africa. Maternal education, wealth index, community women education, and community media exposure were significantly associated with zinc utilization. Increased mass media exposure, maternal education and wealth index is recommended to improve zinc utilization among under-five children with diarrhea.