Allium cepa Linn. (onion), a widely consumed Allium species and a long-standing component of traditional medicine, is rich in bioactive phenolic compounds. The present study aimed to investigate the fertility-enhancing effects of A. cepa extract on reproductive outcomes across two rat generations (F0 and F1). The extract was first subjected to in vitro antioxidant evaluation using DPPH and ROS assays, followed by in vivo toxicity testing. For the fecundity experiment, eighteen male-female rat pairs (n = 36, F0) were assigned to three groups and administered either 75 mg/kg, 150 mg/kg A. cepa extract, or saline control throughout the pre-cohabitation, cohabitation, gestation, and lactation phases. Reproductive parameters such as body weight, fertility index, live birth index, and litter size were recorded. Haematological indices, hormonal levels (FSH, LH, Testosterone, Estradiol), antioxidant status (SOD, glutathione peroxidase), lipid profile, and reproductive organ histology were evaluated in both F0 and F1 generations. The ethanolic extract demonstrated strong antioxidant potential in vitro. Long-term exposure did not alter body weight, fertility index, litter size, or survival index; however, significant improvements were observed in semen pH, sperm motility, count, viability, and volume in both generations. At 150 mg/kg/day, A. cepa extract markedly enhanced fecundity in males and females, as reflected by elevated haemoglobin, FSH, LH, testosterone, and glutathione peroxidase (p < 0.05), alongside reductions in total lipid, LDL, and cholesterol (p < 0.05). Histological analysis revealed improved spermatogenesis and folliculogenesis with healthier tissue architecture. Collectively, these findings indicate that A. cepa extract enhances reproductive performance in rats, likely through modulation of hormonal activity and reduction of oxidative stress.