Background Micronutrient deficiencies are identified among obese individuals. Vitamin D deficiency is prevalent in obese children, and is hypothesized to cause insulin resistance and metabolic abnormalities. This study aimed to determine the effect of vitamin D supplementation on obesity and related metabolic abnormalities among obese Sri Lankan children.Methods A triple-blind randomized controlled trial was conducted among vitamin D deficient (< 20 ng/ml), obese children (n = 96). Children were randomly allocated to three intervention arms - treatment arm receiving weekly vitamin D2 50,000 IU; supplementation arm receiving 2500 IU weekly and control arm receiving placebo. Anthropometry, percentage fat mass (%FM) and blood pressure were assessed and fasting blood glucose, fasting insulin, lipid profile, ALT, AST, vitamin D, parathyroid hormone and hs-CRP and OGTT with 2-hour random blood glucose and insulin was performed at baseline and after 24 weeks of treatment. Ethics Review Committee of Faculty of Medicine, University of Colombo approved the protocol.Results Waist circumference Z-score, %FM and serum calcium significantly improved across all three arms, ALT significantly improved in treatment and supplementation arms while, BMI Z-score, PTH and vitamin D significantly improved in the treatment arm. Biceps (p = 0.035) and subscapular (0.048) skin fold thickness, vitamin D (p = 0.004) and ALT (p = 0.012) significantly improved in the treatment arm.Conclusions A strict dietary and physical activity regimen could improve some of the anthropometric, body composition and metabolic profiles, but high dose vitamin D, enhances those improvements. Therefore high dose vitamin D seems to potentiate management outcomes of obese children with vitamin D deficiency.Trial registration The study was registered at the Sri Lanka Clinical Trials Registry (SLCTR/2015/017) on 12th September 2015 at https://slctr.lk/trials/slctr-2015-017.