Reproductive disorders are associated with neuroendocrine dysregulation in the hypothalamic-hypophysis-gonadal (HHG) axis, which can result from a defective production and action of the neuropeptide gonadotropin-releasing hormone (GnRH), the master regulator of reproduction. We have previously shown that SELENOT, a new thioredoxin-like selenoprotein highly expressed in endocrine and neuroendocrine cells, plays a role in hormone secretion. However, whether SELENOT is involved in neuroendocrine regulatory mechanisms that impinge on vital functions such as reproduction, is totally unknown. We found that brain SELENOT deficiency results in a very strong decline in fertility and impaired sexual behavior in both male and female mice. In the brain, increased density of GnRH neurons is observed in the hypothalamic preoptic area and in their terminals in the median eminence of both male and female mice. This leads to a marked increase in luteinizing hormone (LH), testosterone (T) and estradiol (E2) levels in male mice, while female animals exhibits a severe estrous cycle disorder and a polycystic ovary syndrome (PCOS)-like phenotype, with an increase in LH and testosterone levels and a decrease in folliculo-stimulating hormone (FSH) and E2 levels. SELENOT deficiency impairs LH pulse secretion in both males and females. These phenotypes are reverted after administration of a GnRH antagonist. These results demonstrate for the first time the direct role of a selenoprotein in the neuroendocrine control of reproduction and identify a new mechanism in the brain impacting GnRH neurons and leading to male and female reproductive dysfunction.