The present study aimed to determine the prevalence of childhood obesity and overweight in Iranian children under 5 years of age using a systematic review and meta-analysis. Methods: We searched MEDLINE (PubMed), Web of Science, Google Scholar, Scopus, CINHAL, and the Iranian databases, including Scientific Information Database (www.sid.ir), Iranian Research Institute for Information Science and Technology (Irandoc.ac.ir), Iranmedex (www.iranmedex.com), and Magiran (www.magiran.com), for all articles published between January 1989 and August 2017. Sources of heterogeneity were determined using subgroup analysis and meta-regression. Results: Six articles were ultimately included in the meta-analysis to estimate the pooled prevalence, based on which the prevalence of obesity and overweight were estimated to be 8% (95% confidence interval [CI], 6%-10%) and 9% (95% CI, 7%-11%), respectively. The results of the subgroup analysis showed that the prevalence of obesity in boys and girls was 9% (95% CI, 6%-13%) and 7% (95% CI, 4-10%), respectively, and the prevalence of overweight in boys and girls was 10% (95% CI, 5%-15%) and 9% (95% CI, 5%-13%), respectively. Conclusion: Despite high heterogeneity among the results of the articles included in the meta-analysis, the prevalence of obesity and overweight is higher in Iranian children under 5 years of age. Therefore, parents and the health system must pay more attention to the lifestyle, nutritional habits, and physical activity of these children.