The objective of this study was to provide guidelines to clinicians for the evaluation, treatment, and prevention of vitamin D deficiency with an emphasis on the care of patients who are at risk for obesity and diabetes. Our aim was to determine the relationship between vitamin D3 and metabolic syndrome, and investigate the effect of vitamin D3 supplementation on hyperlipidemia, glucose metabolism, and bone mass in pediatric patients with obesity. We conducted a study between January 2018 and January 2020, with a total of 723 children invited to participate. Of these, 283 were in the vitamin D supplement group (SG) and 440 were in the placebo group (PG). We evaluated blood pressure, fasting glucose, high-density lipoprotein, total cholesterol, low-density lipoprotein, and bone mineral density (BMD) in all subjects. We observed that cholesterol, triglyceride, and glucose levels were strongly associated with 25(OH)D3 levels at baseline. After vitamin D3 supplementation, we observed a significant increase in body mass index (BMI) (<i>P</i> = 0.02) and serum 25(OH)D3 (<i>P</i> < 0.01) levels in the vitamin D3 group compared to the placebo group. Additionally, serum lipids such as total cholesterol (<i>P</i> <0.01), HDL-c (<i>P</i> < 0.01), total cholesterol/HDL-c (<i>P</i> < 0.01), LDL-c/HDL-c (<i>P</i> < 0.01), and triglycerides/HDL-c (<i>P</i> < 0.01) were significantly decreased in the vitamin D group compared to the placebo group. Serum vitamin D3 was inversely associated with cholesterol, triglycerides, and fasting glucose. Our results suggest that vitamin D3 supplementation enhances the beneficial effect of hyperlipidemia, glucose metabolism, and bone mass in pediatric patients with obesity.