Melatonin, conventionally accepted as a pineal gland secretion, is a neuromodulator whose physiological concentrations are regulated by circadian rhythms. Alteration in melatonin levels owing to circadian influences is a major regulator of reproductive functions in animal species that are seasonal breeders. Attributing to its antioxidant properties and capability to cross physiological barriers, such as the blood-brain barrier, the blood-testis barrier as well as having almost no toxicity, melatonin finds high relevance in amelioration of male fertility parameters. Melatonin may affect male reproductive functions by influencing the release of hypothalamic gonadotropin-releasing hormone and pituitary luteinizing hormone, which are among the key hormones in regulation of male reproduction. It may directly act on testicular cells to influence testicular functions. The property of melatonin most essential for testicular functions is its ability to scavenge free radicals, thereby preventing testicular oxidative damage. This article summarizes the updated data on the versatility of melatonin as an endogenous rhythm setter, as an antioxidant molecule and its possible physiological impacts in male reproductive functions.