Background <p>Overweight and obese children are risky for developing chronic cardiovascular disorders. Heart rate variability is a valuable indicator of the cardiovascular health.</p> Aim <p>To outline the impact of supplementation of omega-3 on the variability of the heart rate.</p> Methods <p>A randomized interventional control study has been done on 60 overweight and obese children; 30 children were assigned to the interventional group who received omega-3 with the standard recommendations and 30 children were assigned to the control group who received the standard recommendations only. Resting 10 min Holter ECG was done at the start and after 3 months of omega-3 supplementation in both groups to observe and compare the difference in the heart rate variability. In addition, lipid profiles were investigated and compared.</p> Results <p>Difference in measures of the heart rate variability; RMSSD, SDNN, and pNN50 were increased significantly in cases compared to the controls (<i>P</i> value = 0.017, 0.009, and 0.043 respectively). Differences in measures of the lipid profiles differed only in triglycerides which decreased significantly in cases and HDL which increased significantly in the cases (<i>P</i> value = 0.006, 0.005 respectively).</p> Conclusion <p>Our results suggested that omega-3 supplementation might improve cardiovascular health in overweight and obese children.</p> Impact <p><UnorderedList Mark="Bullet"> <ItemContent> <p>This study discloses the importance of supplementation of omega-3 fatty acids as a cardioprotective dietary supplement.</p> </ItemContent> <ItemContent> <p>Omega-3 fatty acids can improve heart rate variability in overweight and obese children.</p> </ItemContent> <ItemContent> <p>Omega-3 fatty acids can also improve the lipid profiles in overweight and obese children.</p> </ItemContent> </UnorderedList></p>