Obesity is invariably accompanied by autonomic dysfunction, although data in pediatric populations are conflicting. We conducted a systematic review and meta-analysis of 12 studies (totaling 1102 participants) comparing obese and normal-weight subjects (5-18 years of age), defined as body mass index >95th or <85th percentile, respectively. Using a random-effects model, we report the standardized mean differences (SMD) of sympathetic and vagal indices, calculated by heart rate variability. Autonomic dysfunction was present in the obese group, based on the average SMD in the standard deviation of sinus intervals (at -0.5340), and on the ratio of low (LF) to high (HF) frequency spectra (at 0.5735). There was no difference in sympathetic activity, but the heterogeneity among the relevant studies weakens this result. SMD in HF (at 0.5876), in the root mean square of successive differences between intervals (at -0.6333), and in the number of times successive intervals exceeded 50ms divided by the total number of intervals (at -0.5867) indicated lower vagal activity in the obesity group. Thus, autonomic dysfunction is present in obese children and adolescents, attributed to lower vagal activity. Further studies on autonomic function are needed in various pediatric cohorts, placing emphasis on sympathetic activity.