The human reproductive system can be affected by occupational exposure to many physical and chemical risk factors. This study was carried out to review the studies conducted on the issue of the pathophysiological effects of occupational physical and chemical risk factors on the reproductive system of females and males. In this systematic review, the databases such as “Google Scholar,” “Pub-Med,” “Scopus,” and “Web of Science” were used. Following the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA 2020), the studies included in our study were published between 2000 and 2021. In order to extract the required data, all sections of the articles were reviewed. Out of 57 articles we reviewed, 34 articles were related to field studies and 23 articles to clinical studies. Among them, 43 studies dealt with the pathophysiological effects of chemical agents, six studies dealt with the pathophysiological effects of physical factors, and 8 studies dealt with the pathophysiological effects of physicochemical factors on the human reproductive system. Physical (noise, heat, and radiofrequency radiation) and chemical (such as carbamate and organophosphate pesticides, benzene, toluene, xylene, formaldehyde, NO2, CS2, manganese, lead, nickel, and n-hexane) risk factors had pathophysiological effects on the human reproductive system. The presence of these risk factors in the workplace caused damage to the human reproductive system. The rate of these negative pathophysiological effects can be reduced by performing appropriate managerial, technical, and engineering measures in work environments.