Objectives: This study aims to assess the zinc deficiency prevalence in Iran during the past two decades and compare it with other countries. Methods: We searched PubMed, Google Scholar, Web of Sciences, Scientific Information Database (SID), and Magiran for English and Persian reports on zinc deficiency prevalence in Iran. The search terms were “zinc”, zinc deficiency”, “low zinc level”, “low zinc concentration”, “prevalence”, “epidemiology”, “status”, “Iran”, “Iranian”, and “Persian”, using Boolean operators ‘AND’ or ‘OR.’ The preferred reporting items for systematic reviews and meta-analysis (PRISMA) checklist were applied during the review. Two authors reviewed the articles independently. We included all articles published from 2001 to 2021 that reported zinc deficiency prevalence based on serum zinc levels (μg/dL) in the Iranian population. We excluded clinical intervention studies and studies on pregnant women, children with stunting or malnutrition, and patients with a particular disease. The effect sizes of prevalence rates were extracted from original studies. Meta-analysis with the random-effects model was used to estimate the pooled prevalence of zinc deficiency. Publication bias was evaluated by Egger’s test and the Funnel plot. Results: This systematic review and meta-analysis included 20 studies (12 for males, 13 for females, and 18 for both that involved 16138 participants; 8424 males and 9053 females). Using the random effect model, the overall prevalence of zinc deficiency in the general population was 16% (95% CI, 11%-20%), and in males and females, 18.4% (95% CI, 0.12%-0.24%) and 15% (95% CI, 10%-20%), respectively. In subgroup analysis, the prevalence rates of zinc deficiency for 6 years old children and adolescents were 29% and 12%, respectively. Conclusions: The overall prevalence of zinc deficiency in the Iranian population was 16%, lower than the 20% set by IZiNCG (the International Zinc Nutrition Consultative Group) to indicate the need for national intervention programs. However, the COVID-19 pandemic and climate changes threaten this fragile margin. Dietary diversification/modifications, supplementation programs, fortification, and bio-fortification can be used to minimize the problem in high-risk populations. Since this study evaluates the adult healthy population of Iran, we should be cautious about generalizing its results on other population groups like children.