Aim: Arteriosclerotic cardiovascular disease, one of the world’s leading causes of death, first manifests itself at an early age. The identification of children who may have increased cardiovascular risk in the future could be an important prevention strategy. Our aim was to assess the clinical, analytical, and dietary variables associated with arterial stiffness (AS), measured by carotid-femoral pulse wave velocity (cfPWV) in a prepubescent population with metabolically healthy obesity (MHO). Subjects and Methods: A cross-sectional study in prepubescent subjects with obesity who had ≤1 metabolic syndrome criteria (abdominal perimeter and blood pressure ≥90th percentile, triglycerides >150 mg/dL, HDL-cholesterol <40 mg/dL, fasting plasma glucose ≥100 mg/dL) was conducted. Adherence to Mediterranean Diet, blood pressure, BMI, waist/height ratio (WHtR), glycemic status, lipid profile, and cfPWV were analyzed. 75 MHO children (boys: 43; girls: 32; p = 0.20) (age = 10.05 ± 1.29 years; BMI = 25.29 ± 3.5 kg/m2) were included. Results: We found a positive correlation between cfPWV and weight (r = 0.51; p < 0.0001), BMI (r = 0.44; p < 0.0001), WHtR (r = 0.26; p = 0.02), fasting insulin levels (r = 0.28; p = 0.02), and insulin resistance (Homeostatic Model Assessment of Insulin Resistance (HOMA-IR) index) (r = 0.25; p = 0.04). Multiple linear regression analysis identified BMI and HOMA-IR as independent parameters associated with cfPWV. Conclusions: Prepubescent children with obesity who were shown to be metabolically healthy presented with arterial stiffness, which is closely related to BMI and the state of insulin resistance.