Obese children present a higher cardio-metabolic risk. Measuring vascular biomarkers that assess the evolution of arterial stiffness, subclinical atherosclerosis, and hypertension in such patients could be helpful in the long term. We studied 84 children, aged from 6 to 18 years: 50 obese subjects, versus 34 of normal weight. Clinical examination involved: BMI, waist circumference, waist-to-height ratio, and detection of the presence of acanthosis nigricans and irregular menstrual cycles (the latter in adolescent girls). The carotid intima-media thickness (CIMT) was measured with the Aixplorer MACH 30 echography device. The pulse wave velocity (PWV), augmentation index (AIx), and peripheral and central blood pressures (i.e., SBP, DBP, cSBP, cDBP, and cPP) were acquired through a Mobil-O-Graph device. Obese subjects underwent body composition analysis with a Tanita BC-418. Blood tests were: HOMA-IR, lipid panel, uric acid, and 25-OH vitamin D. All vascular biomarkers presented increased values in obese subjects versus controls. The following cut-off values were significant in detecting obesity: for PWV > 4.6 m/s, cSBP > 106 mmHg for the <12-year-olds, PWV > 4.5 m/s and cSBP > 115 mmHg for the 12–15-year-olds, and PWV > 5 m/s, cSBP > 123 mmHg for the >15-year-olds. AIx is higher in obese children, regardless of their insulin resistance status. Waist circumference and waist-to-height ratio correlate to all vascular parameters. HOMA-IR is an independent predictor for all vascular parameters except CIMT. Cut-off values for PWV of >4.8 m/s, SBP > 125 mmHg, and a cSBP > 117 mmHg predicted the presence of acanthosis nigricans. Obese girls with irregular menses displayed significantly higher PWV, SBP, and DPB. Elevated levels of uric acid, LDL-c, non-LDL-c, triglycerides, and transaminases, and low levels of HDL-c and 25-OH vitamin D correlated with higher arterial stiffness and CIMT values. We conclude that CIMT and the markers of arterial stiffness are useful in the early detection of vascular damage in obese children.