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Background Antibiotic resistance is associated with longer hospitalizations, higher treatment costs, and increased morbidity and mortality rates. Purpose This study aimed to determine the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) in Iranian children. Methods International databases, including Web of Science, PubMed, Embase, and Scopus, and Iranian databases, including Scientific Information Database (www.sid.ir), Magiran, and Iranian Database for Medical Literature (idml.research.ac.ir), were systematically searched for articles published between January 2000 and August 2019. Sources of heterogeneity were determined using subgroup analysis and meta-regression. Results Overall, 343 studies were identified; of them, 20 were included in the meta-analysis to estimate the pooled prevalence. The pooled prevalence of MRSA was 42% (95% confidence interval [CI], 29–55) among culture-positive cases of S. aureus, 51% (95% CI, 39–62) in hospitalized children, and 14% (95% CI, 0.05–27) in healthy children. Conclusion The overall pooled prevalence of MRSA in children was 42%. Appropriate infection control measures and effective antibiotic therapy are needed.