Background: Polycystic ovary syndrome (PCOS) is a heterogeneous disorder of reproductive, endocrine, and metabolic functions. Vitamin D has an influence on metabolic and reproductive functions. This study was designed to explore the levels of free 25 hydroxycholecalciferol [25(OH)-D] in PCOS patients. We also aimed to clarify the impact of vitamin D supplementation on cardio-metabolic status, androgen profile, and clinical features of PCOS. Results: Our results revealed significant lower levels of serum 25(OH)-D in PCOS women compared with healthy controls. Even more importantly, our results reported that 25(OH)-D levels were negatively correlated with cardiometabolic risk factors, androgenic profile, and clinical features of PCOS. Stepwise multiple linear regression analysis revealed that carotid intima-media thickness (CIMT), fasting serum insulin (FSI), and fasting plasma glucose (FPG) were the main predictors of 25(OH)-D levels among other clinical and laboratory biomarkers. Considering the impact of VD supplementation in the PCOS group, there were significant improvements of cardio-metabolic risks, PCOS phenotype, and androgenic profile. Even more important, these results are associated with increasing 25(OH)- D serum levels after VD supplementations. Logistic regression analysis observed that androstenedione, FSI, and hirsutism score were independent predictors of response to VD supplementation. Conclusion: The supplementation of VD for 12 weeks improved the cardio-metabolic and androgenic profiles of PCOS.