Background Polycystic ovarian syndrome (PCOS) is a common endocrine disorder affecting women of reproductive age. It is characterized by dyslipidemia, hormonal imbalances, and metabolic dysfunctions.Vitamin D deficiency may be implicated in the pathogenesis of PCOS, potentially exacerbating its metabolic syndrome. However, the exact interplay between these factors remains underexplored. Aim This study aimed to evaluate serum levels of vitamin D and its association with modalities of PCOS among women with PCOS and healthy controls. Methods This was a hospital-based case-control study where 60 women newly diagnosed with PCOS and 56 non-PCOS controls were consecutively recruited within a 10-month period. The women aged 20-40 were recruited at the gynecology clinics of Lagos State University Teaching Hospital and Lagos Island Maternity Hospital. PCOS was diagnosed using the Rotterdam's criteria. The biodata, anthropometry, clinical features, serum vitamin D, cortisol, progesterone, testosterone, estradiol, prolactin, anti-Mullerian hormone (AMH), thyroid-stimulating hormone, follicle-stimulating hormone (FSH), luteinizing hormone (LH), insulin, fasting blood glucose (FBG), total cholesterol (TC), high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), triglyceride (TG), and very-low-density lipoprotein cholesterol (VLDL-C) levels of PCOS-diagnosed women were assessed and compared with those of women without PCOS. The exclusion criteria comprised known diabetics, women with gynecological pathologies such as fibroids, and womenon medications affecting the study analytes or hormones. Statistical analyses included chi-square or Fisher's exact tests for categorical variables, student t-test for continuous variables, and Pearson's correlation for assessing relationships between continuous variables. The significance level was set at p<0.05 and a confidence interval of 95%. Results Individuals with PCOS exhibited a younger mean age (26.90±3.73 versus 29.95±5.00 years, p=0.001) and a higher prevalence of irregular menstrual patterns (46.7% versus 14.3%, p=0.0001) and acne (58.3% versus 37.5%, p=0.025). Moreover, PCOS was associated with elevated levels of TC (p = 0.03), TG (p = 0.03), LDL-C (p = 0.014), FBG (p = 0.001), LH:FSH ratio (p = 0.002), AMH (p = 0.0001), and testosterone (p = 0.003), but low progesterone (p = 0.001) and vitamin D (p = 0.033), alongside a higher incidence of vitamin D deficiency (33.3% versus 26.1%) and insufficiency (66.7% versus 56.5%). Additionally, significant but weak correlations were observed between serum vitamin D levels and waist-hip ratio (r = 0.4, p = 0.016) and FBG (r = -0.4, p = 0.036) in the PCOS group, suggesting potential metabolic implications. Conclusion The PCOS subjects in this study had decreased vitamin D and progesterone levels, with elevated concentrations of testosterone, AMH, lipid profile (TC, LDL, and TG), FBG, and LH:FSHratio. Studies on the therapeutic effect of vitamin D administration in managing PCOS will need to be further evaluated.