The hypothalamic Kiss1 system is an essential component of the hypothalamic-pituitary-gonadal axis, which regulates reproductive function by promoting the secretion of GnRH. Recent studies have identified the effects of prenatal stress on the reproductive function of male offspring. However, the mechanisms underlying the prenatal stress-induced decrease in reproductive function in male offspring remain elusive. Treatment of the hypothalamic Kiss1 system may improve the reproductive function of prenatally stressed male offspring. This review will discuss the potential role of the Kiss1 system in prenatal stress-induced abnormal reproductive function in male offspring.