Background This study aimed to comprehensively analyze the overall congenital heart disease (CHD) prevalence in live births and children in Iran, along with evaluating the spatial distribution of CHD birth prevalence across various geographical regions within the country. Methods A Bayesian hierarchical meta-analysis (PROSPERO 2022: CRD42022331281) was performed to determine the pooled prevalence. A systematic search was conducted using ISI Web of Science, Science Direct, PubMed, IranDoc, SID, and Magiran until October 4, 2023. Crosssectional and cohort studies in both English and Persian languages, focusing on the age range of 0-10 years, were considered for the study population. The study quality was evaluated using the Agency for Healthcare Research Quality (AHRQ) Risk of Bias tool. Heterogeneity was assessed by I² and τ² statistics, and publication bias by Egger’s and Begg’s tests. Results The meta-analysis included 62 studies, revealing an overall CHD prevalence of 2.5 per 1000 births. Over time, CHD birth prevalence in Iran has consistently increased. Spatial distribution analysis, including spatial autocorrelation and local spatial autocorrelation, indicated no spatial clustering (P-value = 0.46) or aggregation (P-value = 0.65) among Iran’s provinces. Geographic disparities were significant ((P-value = 0.000), with the northern and eastern regions showing the highest and lowest CHD prevalence, respectively. Conclusion The overall CHD prevalence in Iran is lower than global rates, but it continues to rise. Furthermore, there are variations in birth prevalence among different regions of Iran. Environmental, genetic, socioeconomic, and diagnostic accessibility differences are possibly involved in regional variation. The limitations like heterogeneity among studies, the potential inaccuracy of reports due to limited use of accurate diagnostic methods in some studies, and the absence of population-based models to investigate prevalence, underscore the urgent need for standardized diagnostic approaches, and the utilization of population-wide birth defect registries to accurately assess CHD prevalence in Iran.