Background Medical errors are considered as a major threat to patient safety. To clarify medical errors’ status in Iran, a review was conducted to estimate the accurate prevalence of medical errors. Methods A comprehensive search was conducted in international databases (MEDLINE, Scopus and the Web of Science), national databases (SID, Magiran, and Barakat) and Google Scholar search engine. The search was performed without time limitation up to January 2017 using the MeSH terms of Medical “error(s)” and “Iran” in Endnote X5. Article in English and Persian which estimated the prevalence of medical errors in Iran were eligible to be included in this review. The JBI appraisal instrument was used to assess the quality of included studies, by two independent reviewers. The prevalence of medical errors was calculating using random effect model. Stata software was used for data analysis. Results In 40 included studies, the most frequent occupational group observed were nursing staff and nursing students (21 studies; 52% of studies). The most reported type of error was medication error (25 studies; 62% of studies, with prevalence ranged from 10 to 80%). University or teaching hospitals (30 studies; 75% of studies) as well as, internal/intensive care wards (10 studies; 25% of studies) were the most frequent hospitals and wards detected. Based on the result of the random effect model, the overall estimated prevalence of medical errors was 50% (95% confidence interval: 0.426, 0.574). Conclusion Result of the comprehensive literature review of the current studies, found a wide variation in the prevalence of medical errors based on the occupational group, type of error, and health care setting. In this regards, providing enough education to nurses, improvement of patient safety culture and quality of services and attention to special wards, especially in teaching hospitals are suggested. Electronic supplementary material The online version of this article (10.1186/s12913-019-4464-8) contains supplementary material, which is available to authorized users.