Background and aim The endocrine disruptor compound bisphenol A (BPA) affects spermatogenesis and exacerbates benign prostate hyperplasia induced by testosterone. Nonetheless, the direct effect of BPA on prostate and testicular cells is not fully investigated. The objective of this study was to evaluate the pathogenic effects of BPA on the structure of the prostate and the ultrastructure of the testis of adult male albino rats via immunohistochemical and transmission electron microscopic study and the potential protective effect of CoQ10 supplementation. Methods A total of 30 male albino Wistar rats were categorized into five equal cohorts: group I, no treatment; group II was administered corn oil; group III received coenzyme Q10 (CoQ10); group IV was administrated BPA; and group V received BPA+CoQ10. Results BPA administration significantly decreased the mean values of the plasma fertility hormones and serum antioxidant enzymes and increased malondialdehyde. BPA administration markedly affected seminal parameters. Coadministered CoQ10 significantly reversed these biochemical changes. BPA induced histopathological alterations in the epithelium and connective tissue of prostate. Immunohistochemistry of the prostate revealed decreased E-cadherin and increased vimentin expressions in BPA-treated group. Ultrastructural analysis of the testis showed impairment of the basal lamina of seminiferous tubules and tight junctions between Sertoli cells after BPA exposure. Conclusion The biochemical and histopathological results of this study revealed direct evidence for BPA-induced male reproductive toxicity in the testes and prostate, causing male infertility. CoQ10 coadministration with BPA partially protects against its damaging effect mediated via its antioxidant capabilities.