Background: The need for informed policymaking highlights the importance of data on human immunodeficiency virus (HIV) prevalence on key populations. In this systematic review and meta-analysis, we aimed to provide an overview of HIV prevalence in men who have sex with men (MSM) in Iran. Methods: We searched literature published between January 2008 and December 2019 to identify studies reporting the prevalence of HIV infection or acquired immunodeficiency syndrome (AIDS) in a population of adult Iranian men with history of sexual contact with other men. We employed Metaprop command in Stata to pool proportions from different studies. Results: Among the 16 studies retrieved, 2 were performed on MSM population directly, 7 among people who inject drugs, 4 among prisoners, 2 among the homeless, and 1 among methamphetamine users. HIV prevalence was 7% (95% CI, 5%-10%) based on the meta-analysis, although noticeable heterogeneity existed because of target population, study year, and study location, which imposed limitations to provide a robust summary measure for the prevalence of HIV. Conclusion: There is a potential risk of observing a high prevalence of HIV in MSM that could hamper the results of various preventive strategies and their achievements in other subpopulations.