The hypothalamus plays a central role in regulating fertility through its interactions with the hypothalamic-pituitary-gonadal (HPG) axis. This review provides a comprehensive analysis of the effects of fertility agents, including herbs and pharmaceutical drugs, on the hypothalamus and its role in fertility regulation. The hypothalamus directly influences the HPG axis by secreting GnRH, a hormone crucial for sexual development and ovulatory cycles. GnRH can be secreted in pulsatile or surge modes, with distinct implications for reproductive function. The HPG axis further regulates reproductive organs and hormonal production, affecting processes like oocyte maturation, ovulation, and steroid hormone synthesis. Herbal remedies have been used historically in various cultures to address fertility issues. Several plants, such as Withania somnifera, Punica granatum, Camellia sinensis, Matricaria chamomilla, Vitex agnus-castus, and Nigella sativa, have been studied for their potential to enhance fertility by modulating the HPG axis and influencing sex hormone levels. Pharmaceutical fertility drugs like clomiphene citrate and metformin also have a significant impact on the hypothalamus. Clomiphene citrate acts as a partial estrogen agonist in the hypothalamus, leading to increased gonadotropin-releasing hormone (GnRH) production and subsequent elevation of gonadotropin levels. Metformin, primarily used for diabetes management, can restore ovarian function in women with polycystic ovary syndrome (PCOS) and improve pregnancy outcomes. Understanding the intricate interactions between fertility agents and the hypothalamus is crucial for developing effective treatments for infertility and optimizing reproductive health.