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Background: Chlamydia trachomatis infection is one of the most common sexually transmitted diseases. There is widespread evidence in recent years that indicates C. trachomatis infection plays a role in sperm dysfunction and poor sperm quality. However, some controversial documents have argued the role of infection with this bacterium in male infertility. Methods: A full comprehensive electronic search was performed using the online databases Web of Science, PubMed, Scopus, Embase, and Google Scholar, without considering the time limits. Results: In the present study, 56 articles were finally found to be eligible. The prevalence of C. trachomatis infection in the infertile males was estimated at 20.6% (19.8-21.5 with 95% CIs; p-Value: 0.01; I2: 97.77; Q-Value: 237.8; p-Value: 0.01; Begg's p-Value: 0.09; Egger's p-Value: 0.01) in overall. We have also shown that infection with C. trachomatis can significantly increase the risk of infertility in men (OR: 2.28; 1.90-2.72 with 95% CIs; p-Value: 0.001; I2: 81.61; Q-Value: 59.81; p-Value: 0.01; Begg's p-Value: 0.73; Egger's p-Value: 0.61). Conclusion: We showed a high prevalence of C. trachomatis in the sperm and semen samples of infertile men, and C. trachomatis infection is associated with a significantly higher risk of infertility in men.