Polycystic ovarian syndrome is a multidisciplinary endocrinopathy of reproductive-aged women that provokes insulin resistance, hyperandrogenism, cardiovascular problems, obesity, and menstrual complications. The present study was designed to investigate the effectiveness of ethanolic extract of Fagonia indica in letrozole-induced PCOS young adult female rats. HPLC was carried out to find the phenolic and flavonoid content of the ethanolic extract of Fagonia indica. Twenty-five female rats were taken and initially divided into two groups: group I (control group) and group II (PCOS group). PCOS was induced by letrozole given orally by gavage. Body weight was recorded weekly and vaginal cytology was analyzed daily. After induction of disease, the PCOS group is further divided into four groups (n = 5): group II (positive control with PCOS), group III (metformin 20 mg/kg treated group), group IV (ethanolic extract of Fagonia indica 500 mg/kg treated group), and group V (metformin plus Fagonia extract). At the end of experimental period, the blood sample of each rat was collected and serum was separated by centrifugation. Afterwards hormonal analysis, lipid profile and liver functioning tests were performed. Ovaries were removed and preserved for histopathological findings while the liver of each rat was stored for the determination of antioxidant potential assessment. Fagonia indica was found to possess quercetin as one of the major flavonoid phytoconstituents. The plant extract exhibited its beneficial effects by restoring hormonal balance, lipid profile, and liver functioning markers. Treatment with F. indica reduced body weight, resolved ovarian cysts, and showed positive effects on follicular growth. Treatment with plant also increased the levels of antioxidant enzymes. This study validates the potential of Fagonia indica for the amelioration of metabolic, as well as, hormonal disturbances that occurred in PCOS.