Pesticides play a crucial role in protecting crops and increasing yield, but unintended exposure can lead to adverse effects, especially on human health. High oxidative stress and inflammation can disrupt the hypothalamic-pituitary-gonadal axis, an important system for impacting gonadal activation, spermatogenesis, pubertal onset and fertility. This study aims to explore the testicular damage and changes in the hypothalamic-pituitary-testicular axis induced by subacute oral exposure to methomyl, as well as the potential protective effects of quercetin. The rats were divided into four groups: control (CO), methomyl-exposed (Meth), quercetin-treated (Qu), and methomyl plus quercetin (Meth/Qu). The methomyl group showed testicular apoptosis and decreased levels of pituitary and gonadal hormones, including follicle-stimulating hormone (FSH), luteinizing hormone (LH), and testosterone, along with elevated levels of pro-inflammatory cytokines (IL-1β, IL-6 and TNF-α) and the pro-apoptotic marker caspase-3. Quercetin treatment alleviated these effects, improved hormone levels, and reversed methomyl-induced testicular damage. This study highlights the potential of quercetin, a nutritional anti-inflammatory substance, in mitigating methomyl-induced physiological disturbances.