Obesity and increasing of arterial stiffness are known as independent risk factors for cardiovascular disease. Previously, we demonstrated that dietary modification or aerobic exercise training can decrease arterial stiffness in obese individuals. However, it has not been compared the effect of dietary modification and/or aerobic exercise training on arterial stiffness in obese men. We compared the effect of three patterns of lifestyle modification (i.e., dietary modification, aerobic exercise training or combined them) on arterial stiffness in obese men. Fifty-three obese men completed the 12-week lifestyle modification program, dietary modification (D), aerobic exercise training (E) or combined D and E (DE). Before and after the program, all participants were measured central, peripheral, and systemic arterial stiffness (measured by carotid-femoral pulse wave velocity [cfPWV], femoral-ankle PWV [faPWV] and brachial-ankle PWV [baPWV]). We demonstrated that the degree of decrease in BMI was the greatest after DE, and that was greater after D than E. The level of decrease in baPWV after DE was the greatest among three interventions. On the other hand, the level of decrease in baPWV in D group was similar to E group. These results suggested that systemic arterial stiffness may be decreased by different mechanisms between D and E groups. We demonstrated that dietary modification decreased central and systemic arterial stiffness, and aerobic exercise training decreased central, systemic, and peripheral arterial stiffness in obese individuals. We also showed an additional effect of decreasing systemic arterial stiffness by combining dietary modification and aerobic exercise training in obese individuals.