Background: Vitamin D deficiency is an important risk factor for some chronic disease. Some reports suggested that there is an interrelationship between lipids and cholecalciferol. Objectives: This meta-analysis was conducted to summarize the existing evidence of randomized controlled trial (RCTs) to evaluate the effect of vitamin D supplementation on lipid profiles in children and adolescents. Methods: In this systematic review and meta-analysis data base such as Web of Science, PubMed, Scopus, Google Scholar, EMBASE, Science Direct, Magiran, SID were searched for studies prior up to December 21st, 2019. This study was conducted according to PRISMA guidelines. I-square was used to measure the existing heterogeneity through included articles. Considering heterogeneity among articles, random-effect models were applied to pool standardized mean differences (SMD) as overall effect size. P-value <0.05 was considered statistically significant. The analyses were conducted by STATA v 14.0. Study eligibility criteria included Children and adolescents (<18 years) and evaluated the association between vitamin D and lipid profile. Results: A total of 13 trials (number of participant=173) were included in the current meta-analysis. The SMD is 0.23, the vitamin D supplementation is associated with significant slight increase in high-density lipoproteins (HDL) levels in children and adolescent (SMD 0.23; 95% CI, 0.02, 0.45, P= 0.036; I2= 57.7%, Egger’s P=0.554). We found no significant association between vitamin D supplementation and LDL-cholesterol levels (SMD -0.10; 95% CI, − 0.29, 0.09, P = 0.310 ; I2 = 0.0%, Egger’s P=0.689), Total cholesterol  levels (SMD –0.01; 95% CI, − 0.20, 0.18, P = 0.926 ; I2 = 0.0%, Egger’s P=0.005) and triglycerides levels (SMD -0.10; 95% CI, − 0.22, 0.02, P = 0.093 ; I2 = 0.0%, Egger’s P=0.160). Conclusions and implications: vitamin D could marginally increase HDL level, without any significant effect on LDL-C, TG, and TC levels.