Aerobic exercises are considered as an effective method of improving several undesirable health outcomes; however, their implications in the male reproductive axis have remained controversial. The present study evaluated the impact of physical exercise on the male reproductive system in rats and investigated the potential central and peripheral mechanisms involved in it. Twenty male Sprague–Dawley rats were randomly divided into control and exercise groups, with 10 rats per group. The rats were subjected to a swimming exercise for 60 min/day for five days a week and the protocol was followed for six constitutive weeks. We found that the swimming exercise significantly decreased the testicular weight and the testicular somatic index. Furthermore, there was a marked reduction in several sperm characteristics, including sperm count, motility, morphology, and viability in the exercised rats. The serum levels of reproductive hormones, i.e., testosterone (T), luteinizing hormone (LH), and follicle stimulating hormone (FSH) were significantly decreased. A histological examination of testes and epididymis revealed defective spermatogenesis. Molecular analysis revealed the downregulation of the expression of mRNAs of the hypothalamic kisspeptin (Kiss1), Kiss1 receptor (Kiss1r), gonadotropin-releasing hormone (GnRH1), GnRH1 receptor (GnRHr), and testicular Kiss1r along with an upregulation in the gene expression of GnRHr in the pituitary. We also observed a significant reduction in the activity and the expression of mRNAs of testicular superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GPx) and a marked elevation in the levelsof malondialdehyde (MDA). These findings implied that chronic swimming exercise suppressed the Kisspeptin–GnRH signaling pathway, consequently reducing the production of male reproductive hormones. A simultaneous increase in the oxidative stress could contribute to exercise-induced inhibition of male reproductive functions. To conclude, an appropriate training program is important to maximize the benefits and minimize the side effects of physical exercises on the male reproductive system.