Background: ‘Polycystic ovarian syndrome (PCOS) is a prevalent endocrine disorder among women of reproductive age’. ‘It is characterized by hyperandrogenism, menstrual irregularities, and metabolic dysfunction, which predispose patients to endometrial abnormalities’. Despite extensive research on its metabolic and reproductive effects, the relationship between PCOS and endometrial pathology requires further exploration. The objective was to evaluate the clinical, hormonal, metabolic, and histological indicators of endometrial abnormalities in women with PCOS and compare them to healthy controls. Methodology: A cross-sectional study was conducted at Hayatabad Medical Complex, including 120 participants divided into two groups: 60 ‘women with PCOS diagnosed based on Rotterdam criteria and 60 healthy controls’. Data collection involved clinical evaluation, hormonal and metabolic profiling, ultrasound assessment, and histological examination of endometrial biopsies. ‘Statistical analysis was performed using SPSS version 25, with significance set at p < 0.05’. Results: ‘Women with PCOS had significantly higher BMI (30.2 ± 5.8 vs. 24.7 ± 4.6; ‘p < 0.001)’ and menstrual irregularities (83% vs. 12%; p < 0.001). Hormonal and metabolic markers, including LH/FSH ratio (2.9 ± 1.2 vs. 1.3 ± 0.4; p < 0.001), estradiol (63.2 ± 14.5 vs. 49.5 ± 11.8 pg/mL; p < 0.001), and HOMA-IR (4.3 ± 1.6 vs. 2.2 ± 0.8; p < 0.001), were significantly elevated in the PCOS group. Endometrial thickness was greater in women with PCOS (12.5 ± 3.3 mm vs. 8.9 ± 2.6 mm; p < 0.001). Histological abnormalities, including hyperplasia with atypia (15% vs. 2%; p < 0.001) and endometrial carcinoma ‘(5% vs. 0%; p = 0.014), were more prevalent in the PCOS group’. Conclusion: Women with PCOS are at a higher risk of endometrial abnormalities due to hormonal and metabolic disturbances. Early screening and intervention targeting these risk factors can mitigate the potential for severe endometrial pathologies, including malignancies. Further research should explore the progression of endometrial changes in PCOS and the efficacy of targeted therapeutic approaches.