Abstract Objectives Vitamin D deficiency is common in the pediatric group with obesity and is a risk factor for metabolic syndrome. Supplementation of vitamin D may require higher dosing than in normal-weight children. The aim of our study was to investigate the response of supplementation on vitamin D levels and the metabolic profile in youths with obesity. Methods Children and adolescents with obesity (Body mass index >2.3 SDS, age ≤18 years) and hypovitaminosis D (level <20 μg/L) who entered a residential weight-loss program in Belgium, were included during summer. Subjects were randomized: Group 1 received 6,000 IU vitamin D daily for 12 weeks, whereas Group 2 simultaneously participating in the weight-loss program received no supplementation. Differences in vitamin D levels, weight, insulin resistance, lipid patterns, and blood pressure after 12 weeks were assessed. Results A total of 42 subjects (12–18 years) with hypovitaminosis D were included, group 1 (n=22) received supplementation after randomization. After 12 weeks, a median increase in vitamin D levels of 28.2 (24.1–33.0) and 6.7 (4.1–8.4) µg/L was observed in group 1 and group 2, respectively (p-value<0.001), resulting in vitamin D sufficiency in 100 and 60% of subjects. No significant differences in weight loss (p-value 0.695), insulin resistance (p-value 0.078), lipid patterns (p-value 0.438), or blood pressure (p-value 0.511) were observed between both groups after 12 weeks of treatment. Conclusions Supplementation with 6,000 IU vitamin D daily during 12 weeks in children and adolescents with obesity and hypovitaminosis D is safe and sufficient to reach vitamin D sufficiency. However, no positive effects on weight loss, insulin resistance, lipid patterns, or blood pressure were observed.