Background: Vitamin D deficiency is related to rickets in children, and it can increase the risk of osteoporosis in adulthood. The aim of our study was to estimate the prevalence of vitamin D deficiency among healthy Iranian children and adolescents. Vitamin D levels less than 20ng/ml and between 20 and 30ng/ml was considered as vitamin D deficiency and insufficiency, respectively. Methods: Relevant observational studies evaluating the prevalence of vitamin D deficiency through 1 January 1990 to 28 Dec 2016, were searched in several electronic databases including Iran-Medex, Scientific Information Database (SID), Irandoc, PubMed and NLM Gateway (for MEDLINE), Web of Science, and Scopus with no restriction on language. Only full-text articles were used for data extraction and synthesis after considering the inclusion/exclusion criteria. Results: 11 studies included; the data of four studies of Iranian newborns were withdrawn because of their high heterogeneity. The prevalence of vitamin D deficiency in Iranian boys and girls were 35% (CI 95% 34–37) and 61% (CI 95% 60–63), respectively. The prevalence of vitamin D insufficiency in Iranian children and adolescents was 31% (CI 95% 30–31). Conclusion: It seems that the prevalence of vitamin D deficiency is very high among Iranian children and adolescents. The present findings could provide practical information for healthcare decision makers.