Background: Obese children tend to consume low dietary folate which is an important cofactor in remethylation of homocysteine to methionine, leading to hyperhomocysteinemia. Objective: To determine whether folic acid supplementation could reduce plasma homocysteine in obese children. Design: Obese children aged 9-15 years with body mass index > median plus 2 SD according to the WHO reference were randomly allocated into 2 groups: receiving either 5 mg folic acid or placebo for 2 months. Fasting homocysteine, creatinine, folate, vitamin B12, insulin, glucose and lipid profiles were taken at baseline and the end of study. Dietary folate intake and physical activity were assessed using validated questionnaires. Results: A total of 50 obese children (31 boys) took part in the study. Their mean age was 10.9±1.6 years and mean BMI Z-score was 3.41±0.69. After the intervention, plasma homocysteine decreased by 15.75% and 6.99% in the folic acid and placebo group, respectively (mean difference 8.76%; 95%CI: 0.26%, 17.25%, p= 0.044). This divergence was more pronounced in boys and it remained significant after adjusting for baseline homocysteine and other confounders. Subgroup analysis showed a larger magnitude of plasma homocysteine reduction in the low folate group. Conclusions: The homocysteine lowering effect of folic acid supplementation was found in obese children especially in boys and those with low serum folate. The further long-term interventional study is needed to determine the effect of the lowered plasma homocysteine on the cardiovascular outcomes in obese children.