Background: Polycystic Ovarian Syndrome (PCOS) is a common endocrine disorder affecting women of reproductive age. Menstrual irregularities, hyperandrogenism, and polycystic ovarian morphology characterize it. The condition is often associated with metabolic disturbances such as insulin resistance, obesity, and dyslipidemia. This study aimed to evaluate the biochemical and physiological effects of estrogen and progesterone on ovarian function in PCOS and assess the effectiveness of various treatment strategies. Methods: A cross-sectional study was conducted from January 2023 to January 2024 at Hayatabad Medical Complex, Peshawar, Pakistan, involving 120 women diagnosed with PCOS based on the Rotterdam criteria. Data collection included demographic, clinical, and hormonal evaluations. Hormonal parameters, such as estradiol, progesterone, testosterone, LH/FSH ratio, and AMH, were measured alongside metabolic markers like fasting glucose and lipid profile. Ultrasound assessments were performed to evaluate ovarian morphology and physiological parameters, including follicular development and ovarian blood flow. Participants were treated with hormonal therapies, non-hormonal interventions, or ovulation inducing agents, and responses were assessed after three months. Results: The mean age of participants was 29.5 years, and the average BMI was 28.7 kg/m², indicating a predominance of overweight individuals. Hormonal profiles showed elevated LH/FSH ratios and testosterone levels, coupled with low progesterone and estradiol levels, characteristic of PCOS. Metabolic markers highlighted an increased risk for insulin resistance and dyslipidemia. Treatment resulted in significant improvements in ovulation rates (68%), follicular development (72%), and endometrial thickness (7.5 mm on average). Lifestyle interventions and pharmacological therapies effectively reduce metabolic and hormonal imbalances. Conclusion: This study underscores the multifaceted nature of PCOS and the importance of individualized, multidisciplinary management approaches. Hormonal therapies and lifestyle modifications significantly improved reproductive and metabolic outcomes. Future research should focus on long-term treatment efficacy and explore genetic and environmental factors influencing PCOS.