Background Vitamin D deficiency is a prevalent and important global health problem. Because of its role in growth and development, vitamin D status is likely to be particularly important in adolescent girls. Here, we explored the effects of high-dose vitamin D supplementation on cardio-metabolic risk factors. Methods We have examined the effects of vitamin D supplementation on cardio-metabolic risk factors in 988 healthy adolescent girls in Iran. Fasting blood samples and anthropometric measurements were obtained at baseline and after supplementation with high-dose vitamin D. All individuals took a capsule of 50,000 IU vitamin D/week for nine weeks. The study was completed by 940 participants. Results The prevalence of vitamin D deficiency was 90% at baseline, reducing to 16.3% after vitamin D supplementation. Vitamin supplementation was associated with a significant increase in serum concentrations of 25 (OH) vitamin D and calcium. There were significant reductions in diastolic blood pressure, heart rate, waist circumference and serum fasting blood glucose, total- and low-density lipoprotein-cholesterol after the nine-week period on vitamin D treatment, but no significant effects were observed on body mass index, systolic blood pressure or serum high-density lipoprotein cholesterol and triglyceride. Conclusion Vitamin D supplementation had beneficial effects on cardio-metabolic profile in adolescent girls.