Context Polycystic ovary syndrome (PCOS) is a common endocrine disorder marked by hormonal and clinical imbalances. Genistein (GEN), a soy isoflavone with antioxidant properties, has shown promise in PCOS treatment, although its mechanisms remain unclear. Aims This study aimed to investigate the effects of genistein on ovarian dysfunction in a letrozole-induced PCOS mouse model, focusing on steroidogenesis, apoptosis, and PARP-1 signaling. Methods PCOS was induced by oral administration of letrozole (37.5 mg/kg.day) for 21 days. Mice were then divided into the following three groups (n = 10 each) for another 21-day treatment: control (corn oil), PCOS (continued letrozole), and PCOS + GEN (letrozole + genistein, 50 mg/kg.day, i.p.). Key results Genistein restored estrous cyclicity in 80% of treated mice versus 0% in the PCOS group (P < 0.05). Histologically, it improved follicular morphology, increased granulosa cell thickness and density, and promoted corpora lutea formation. Genistein significantly reduced serum T and P4 concentrations (P < 0.05) and modulated expression of steroidogenic proteins (CYP11A1, CYP19A1, STAR). It also decreased cleaved Caspase-3 and cleaved PARP-1 expression (P < 0.05), and suppressed abnormal PARylation without affecting total PARP-1 expression levels. Conclusions Genistein alleviates ovarian dysfunction in PCOS mice by restoring estrous cyclicity, enhancing follicular development, and normalizing hormone concentrations, through regulation of steroidogenic proteins, inhibition of apoptosis, and modulation of PARP-1 activity. Implications These findings support genistein as a potential therapeutic agent for PCOS, targeting the PARP-1–pADPr axis and apoptosis. Further studies are needed to explore upstream mechanisms and evaluate its long-term effects on reproductive health.