Early obesity predicts initial modifications in cardiac and vascular autonomic regulation. The aim of this study was to assess the possible interaction between non-invasive measures of autonomic cardiovascular control and peripheral endothelium regulation in children with overweight and obesity. We involved 114 young subjects (77M/37F, 12.7 ± 2.2 years) with normal weight (NW, n = 46,) to overweight or obesity (OB, n = 68). Multivariate statistical techniques utilizing a collection of modern indices of autonomic regulation, adiposity indexes and metabolic profile were employed. Resting values show substantial equivalence of data. Conversely, blood pressure variance is greater in NW/OB groups. The correlation matrix between major autonomic and metabolic/hemodynamic variables shows a clustered significant correlation between homogeneous indices. A significant correlation between metabolic indices and endothelial and autonomic control, mostly in its vascular end, was recorded. Particularly, the alpha index is significantly correlated with triglycerides (r = −0.261) and endothelial indices (RHI, r = 0.276). Children with obesity show a link between indices of autonomic and endothelial function, fat distribution and metabolic profile. The optimization of autonomic control, for instance by exercise/nutrition interventions, could potentially prevent/delay the occurrence of structural vascular damage leading to reduced cardiovascular health.