Busulfan, an alkylating chemotherapeutic agent, is associated with male reproductive toxicity, including impaired spermatogenesis and hormonal imbalance. This study aimed to investigate the protective effects of quercetin, a natural antioxidant flavonoid, against busulfan-induced testicular and epididymal damage in adult male rats. Methods: Forty adult male albino rats were randomly divided into four groups: Control, Quercetin (70 mg/kg), Busulfan (10 mg/kg), and Quercetin +Busulfan. Treatments were administered orally for four weeks. Testicular and epididymal tissues were evaluated histologically, and sperm parameters, oxidative stress markers (MDA, SOD), inflammatory cytokines (TNF-α, IL-10), apoptotic proteins (caspase-3, Bax), antiapoptotic (BCL-2) and serum sex hormones (testosterone, LH,and FSH) were assessed. Results: Busulfan significantly impaired testicular architecture, reduced sperm count and motility, increased MDA levels, and decreased SOD activity. It also elevated pro-inflammatory cytokines and pro-apoptotic markers while suppressing serum testosterone, LH, and FSH levels (p < 0.05). Co-administration of quercetin markedly alleviated histopathological damage, restored sperm quality, reduced oxidative and inflammatory markers, and normalized hormone levels. Conclusion: Quercetin demonstrates significant protective effects against busulfan-induced testicular and epididymal toxicity, likely through its antioxidant, anti-inflammatory, and anti-apoptotic mechanisms. These findings support the potential use of quercetin as an adjuvant therapy to mitigate chemotherapy-induced male infertility.