Background: Polycystic ovary syndrome (PCOS) is a common endocrine disorder and a leading cause of infertility in women. Studies suggest that naringenin may improve ovarian function; however, its molecular mechanism within the hypothalamus-pituitary-gonad (HPG) axis remains unclear. Objectives: This study investigated the role of naringenin on the expression of corticotropin-releasing hormone (CRH) and nesfatin-1 genes in the hypothalamus of PCOS rats. Methods: Twenty rats, each weighing 180 - 200 g, were divided into four groups (n = 5). Polycystic ovary syndrome was induced by administering estradiol valerate (2 mg per rat). The control and PCOS groups received saline, while the other two PCOS groups received intraperitoneal injections of naringenin at doses of 20 and 50 mg/kg for 14 days. Hypothalamic samples were collected to measure gene expression via real-time PCR. Results: The PCOS group showed a significant decrease in CRH and nesfatin-1 gene expression compared to the control group (P ≤ 0.05). Naringenin treatment significantly increased the expression of CRH and nesfatin-1 genes in comparison to the PCOS group (P ≤ 0.05). Conclusions: Naringenin appears to have therapeutic potential in improving ovarian function in PCOS. Its effects are mediated through up-regulation of hypothalamic neuropeptides upstream of GnRH neurons.