To determine the relationship between insulin resistance (IR) and arterial stiffness independent of obesity in male adolescents, we evaluated body fat, lipid parameters, indices of IR (fasting insulin, and the homeostasis model assessment of insulin resistance [HOMA-IR]), indices of insulin sensitivity (IS) (fasting glucose/fasting insulin [GF/IF], and the quantitative insulin sensitivity check index [QUICKI]), and lifestyle parameters in 256 male adolescents. We divided the study group into the following four subgroups based on the median value of HOMA-IR and obesity: non-obese with IS, non-obese with IR, obese with IS, and obese with IR. In order to estimate arterial stiffness, we measured brachial ankle pulse wave velocity (baPWV). Despite having a high body mass index (BMI), obese-IS adolescents showed a significantly lower fasting insulin and baPWV, but had higher IS indices than non-obese-IR adolescents. After an adjustment for age, BMI, waist-to-hip ratio, mean blood pressure, heart rate, total cholesterol level, triglyceride, alanine aminotransferase (ALT) level, physical activity, and television and computer usage, multiple regression models showed that baPWV was independently correlated with IR and IS indices. In conclusion, our results demonstrate an association between IR and baPWV independent of weight, suggesting that IR is a risk factor for the development of early atherosclerosis. Interventions that decrease IR in addition to weight reduction may be necessary to alter the early development of cardiovascular risk.