No data are available on the relationship between subclinical hypothyroidism and risk factors for the development of cardiovascular disease in obese adolescents with nonalcoholic fatty liver disease (NAFLD). This study aimed to determine whether an association exists between subclinical hypothyroidism and risk factors for the development of cardiovascular disease in obese adolescents with NAFLD. The study enrolled 111 obese adolescents and 42 lean subjects. The obese subjects were divided into two subgroups based on the presence or absence of fatty liver with high transaminases: a NAFLD group and a non-NAFLD group. Subclinical hypothyroidism was defined as a thyroid-stimulating hormone (TSH) level higher than 4 mIU/l and a normal free-thyroxine level (0.6-1.8 ng/dl). Insulin resistance was calculated by the homeostasis model assessment (HOMA-IR). Left ventricular mass (LVM), LVM index measurements, carotid intima media thickness (IMT), and HOMA-IR values were higher in the NAFLD obese group with TSH levels higher than 4 mIU/l than in the NAFLD obese group with TSH levels lower than 4 mIU/l. Elevated TSH values in the NAFLD obese group were positively correlated with most of the metabolic and cardiovascular risk parameters such as total cholesterol (r = 0.606, p = 0.001), triglycerides (r = 0.476, p = 0.016), low-density lipoprotein cholesterol (r = 0.461, p = 0.004), insulin (r = 0.607, p = 0.001), HOMA-IR (r = 0.596, p = 0.002), carotid IMT (r = 0.894, p < 0.0001), and LVM (r = 0.563, p = 0.003). The findings demonstrated that the obese adolescents with NAFLD and subclinical hypothyroidism had a more adverse cardiovascular risk profile and a higher carotid IMT and LVM.