To determine the association between epicardial fat thickness and carotid arterial stiffness, carotid intima-media thickness (CMIT), left atrial (LA) volume, and left-ventricular (LV) geometry parameters in obese children and adolescents compared with controls. A case-control study was performed in 96 children and adolescents (obese n = 66, controls n = 30) age 9–16 years old (38 female and 58 male, mean age 11.7 ± 2.8 years) undergoing transthoracic echocardiography and carotid artery ultrasound. Clinical, anthropometric, and biochemical determinations were also recorded. Epicardial fat thickness (2.76 ± 1.2 vs. 1.36 ± 0.7 mm, p < 0.001), LA volume (35.7 ± 13.2 vs. 28.9 ± 9.8 mL, p = 0.008), LV mass (118.3 ± 38.6 vs. 96.4 ± 35.4 mL, p = 0.008), CIMT (0.48 ± 0.07 vs. 0.44 ± 0.05 mm, p = 0.019), and local pulse wave velocity (LPWV; 3.7 ± 0.5 vs. 3.2 ± 0.4 m/seg, p = 0.007) were significantly increased in obese children and adolescents compared with controls. Epicardial fat showed a significant and positive correlation with LA volume, LV mass, and LPWV as well as a significant and independent association with increased CIMT (odds ratio (OR) = 3.19 [1.88–7.99], p = 0.005) in the study population. Epicardial fat thickness is linked to obesity, carotid subclinical atherosclerosis, and cardiac geometry parameters and might be a useful tool for the cardiovascular risk stratification in children and adolescents.