Obesity and arterial stiffness are important risk factors for disease development. However, the relationship between obesity and arterial stiffness remains unclear. We examined the relationship of visceral fat area (VFA) and anthropometric obesity indices with arterial stiffness. This cross-sectional study was conducted among 2 789 participants (50% women) who underwent both VFA and brachial-ankle pulse wave velocity (baPWV) measurements during health checkups. Body mass index (BMI), waist circumference (WC), waist-height ratio (WHtR), a body shape index (ABSI), and body roundness index (BRI) were assessed. Visceral fat area was quantified using abdominal computed tomography. In women, VFA and all anthropometric indices positively correlated with age. In men, VFA, WHtR, ABSI, and BRI positively correlated with age; BMI inversely correlated with age; and WC did not correlate with age. Visceral fat area significantly correlated with anthropometric indices, but its correlation with ABSI was modest. In women, baPWV showed modest correlations with VFA and anthropometric indices and little correlations with BMI. In men, baPWV modestly correlated with VFA, WHtR, ABSI, and BRI, but inversely correlated with BMI and did not significantly correlate with WC. The multivariable-adjusted model showed that VFA and anthropometric indices, except ABSI, were inversely associated with baPWV; however, they were positively associated with metabolic syndrome components, including hypertension, dyslipidemia, and hyperglycemia. A body-shaped index weakly associated positively with baPWV, but misclassified individuals at risk for metabolic syndrome components. Visceral fat area and most anthropometric obesity indices were positively associated with hypertension, dyslipidemia, and hyperglycemia, but inversely associated with baPWV. Visceral fat area and anthropometric indices, except a body-shaped index, were inversely associated with brachial-ankle pulse wave velocity but positively associated with metabolic syndrome components, including hypertension, dyslipidemia, and hyperglycemia.