Background: Children in all countries, especially in developing countries, constitute a vulnerable group. Therefore, attention to their health issues is very important. The aim of this study was to determine the prevalence of stunting in Iranian children under-five years. Methods: All original studies were searched by complex search syntax from international databases including Medline (PubMed), Web of sciences, Google scholar, Scopus, CINHAL and the Iranian databases consist of SID (Scientific Information Database, www.sid.ir), Irandoc (Iranian Research Institute for Information Science and Technology, Irandoc.ac.ir), Iranmedex (www.iranmedex.com), and Magiran (www.magiran.com) from January 1989 to August 2017. Two independent reviewers identified relevant studies in several steps. We employed a random effect model to generate a pooled prevalence. The reported prevalence is presented as percent and 95% confidence interval (CI). Sources of heterogeneity among the studies were determined using subgroup analysis and meta-regression. Results: Finally, 16 studies from different settings remained for meta-analysis in order to have a pooled prevalence estimate, which prevalence of total stunting was 12% (95%CI: 10–14). Subgroup analysis for gender showed that the prevalence of stunting in both boys and girls children were equal to 10% (95%CI: 8–11) and 9% (CI 95% 8–10), respectively. Also pooled prevalence of stunting in southern provinces are higher than other provinces. Conclusion: The prevalence of stunting in some regions of Iran is higher than others. Although, in recent years much effort has been made to address deprivation such as economical, nutritional and social supporting, improvement of the quality of life, there are still nutritional problems in these areas of Iran.