Background: Polycystic ovary syndrome (PCOS) is a prevalent endocrine disorder associated with reproductive and metabolic dysfunction. Vitamin D deficiency, widespread in South Asian populations, may exacerbate clinical and biochemical abnormalities in PCOS. This study aimed to evaluate the association between vitamin D status and clinical as well as metabolic features in PCOS women. Methods: A cross sectional analytical study was conducted over six months (January–June 2025) at a tertiary care hospital in Karachi, Pakistan. A total of 100 women aged 18–35 years with PCOS, diagnosed by Rotterdam criteria, were enrolled. Demographic, anthropometric, and clinical data including menstrual history, hirsutism, and acanthosis nigricans were recorded. Biochemical evaluation included fasting glucose, insulin, HOMA-IR, serum testosterone, LH/FSH ratio, and 25-hydroxyvitamin D [25(OH)D] levels. Vitamin D status was categorized as deficient (<20 ng/mL), insufficient (20–29 ng/mL), or sufficient (≥30 ng/mL). Results: Vitamin D deficiency was observed in 62% of participants, insufficiency in 24%, and sufficiency in 14%. Deficient women had significantly higher BMI, waist circumference, fasting insulin, HOMA-IR, total testosterone, and Ferriman–Gallwey scores compared to sufficient women (p<0.05). Oligo/amenorrhea was more frequent in deficient women (82.3%) versus sufficient women (57.1%). Logistic regression showed that vitamin D deficiency independently predicted insulin resistance (adjusted OR 3.12, 95% CI 1.09–8.94) after adjusting for age and BMI. Conclusion: Vitamin D deficiency is highly prevalent in PCOS women in Pakistan and is significantly associated with obesity, insulin resistance, hyperandrogenism, and menstrual dysfunction. Screening and correction of vitamin D deficiency may improve both reproductive and metabolic outcomes in this population.