Objective: The objective of this systematic review was to assess the effectiveness of different physical exercise interventions on the lipid profile (high-density lipoprotein cholesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C), total cholesterol (TC), and triglycerides (TG)) of obese children. Method: A computerized search was made of seven databases using keywords. Effect sizes (ES) and 95% confidence intervals were calculated, and the heterogeneity (I(2)) of the studies was estimated using Cochran's Q-statistic applied to the effect size means. The studies were grouped according to the intervention program-aerobic alone or combined (aerobic fitness, strength, and flexibility). Results: Seven studies were selected for review as satisfying the inclusion criteria. Six were randomized controlled trials (n=318) and one was a controlled clinical trial (groups not randomly assigned) (n=38). The main cumulative evidence indicates that the programs based on aerobic exercise alone have a moderate (ES=-0.49; I²=87) and a large effect (ES=-0.55; I²=77) on LDL-C and TG concentrations, respectively; and the programs based on combined exercise have a moderate effect (ES=0.50; I²=0) on HDL-C concentration. Conclusions: The programs based on aerobic exercise (60 min, 3 times/week, ≤75% maximum heart rate) improve the LDL-C and TG concentrations. Moreover, the programs based on combined exercise (≥60 min, >75% maximum heart rate) also improve the HDL-C concentration.