Purpose: Wasting and underweight are the 2 main indicators of children's undernutrition. We aimed to estimate the prevalence of undernutrition at the national level in Iran. Methods: We performed a search for original articles published in international and Iranian databases including MEDLINE, Web of Science, Google Scholar, Scopus, CINHAL (Cumulative Index to Nursing and Allied Health Literature), Scientific Information Database, Irandoc, Iranmedex, and Magiran during January 1989-August 2017. Seven keywords, in English and Persian, including malnutrition, protein energy malnutrition, growth disorders, underweight wasting, weight loss, children below 5 years old, and children, were used to search the databases. Results: Finally, 17 articles were included in the meta-analysis, based on which the prevalence of underweight and wasting in Iranian children were estimated to be 11% and 5%, respectively. The prevalence rates of underweight among children in the central, western, southern, and northern parts of Iran and at the national level were 24%, 5%, 20%, 17%, and 6%, respectively. The prevalence rates of wasting in the central, western, southern, and northern parts of Iran and at the national level were 9%, 4%, 11%, 5%, and 4%, respectively. Conclusion: Although the prevalence of underweight and wasting in Iran was low, some parts of the country showed high prevalence. The main reason behind this difference in the prevalence of malnutrition may be due to the level of development in different regions.