The main objective of this cross-sectional study is to assess the cardiac autonomic neural activity in the presence of abnormally increased body weight in youths and its relationship to metabolic risk factors and cardiorespiratory fitness (CRF). Sixty-four overweight and obese patients, aged 9-17 years, of both sexes, stratified according to the international BMI cut-off, were enrolled. Continuous ECG was recorded during 15 min in resting conditions, and the heart rate variability (HRV) was measured in the time domain, frequency domain and for nonlinear dynamics. In addition, cardiometabolic risk factors and CRF in effort conditions were assessed. Among the overweight and obese youths, no significant differences were observed regarding metabolic parameters and heart rate, although CRF was the lowest in the severely obese youths. Likewise, no significant differences were observed in HRV, independent of how it was assessed. A positive and significant relationship, independent of the degree of obesity, pubertal stage and breathing rate under resting conditions, has been observed among sympathovagal balance, insulin and the homeostatic model assessment index. Furthermore, CRF assessed by volume oxygen peak was associated with insulin levels (r = -0.273; P < 0.05), the SD of the NN interval series (r = 0.268, P < 0.05) and the long-term variation using the Poincaré plot (PS1: r = 0.275, P < 0.05; PS2: r = 0.273, P < 0.05). The key findings of the present study were the presence of a link among fasting insulin, HRV and CRF independent of the degree of obesity, indicating the heterogeneity of obese children and adolescents.