The relationship between weight-adjusted-waist index (WWI, a newly developed obesity index) and peripheral arterial disease (PAD) is unclear. We aimed to explore the association between WWI and the prevalence of PAD in US adults. A total of 7,344 participants (males: 50.60%; females: 49.40%) from the 1999–2004 National Health and Nutrition Examination Survey (NHANES) were included in this study. WWI was calculated as waist circumference (WC) divided by the square root of weight. PAD was defined as an ankle-brachial index < 0.90 in either leg. The prevalence of PAD was 7.84%, which was respectively 3.72%, 7.23%, and 12.58% in WWI tertiles 1–3 (P < 0.001). WWI was positively associated with an elevated likelihood of PAD (OR = 1.25, 95% CI: 1.06–1.48), and the association was robust in stratified subgroups (all P for trend > 0.05). For male participants, there was a nearly linear relationship between WWI and PAD (OR = 1.35, 95% CI: 1.01–1.82). However, non-linear positive relationships were detected in females with an inflection point of 10.98 cm/√kg. A positive association was observed on the left of the inflection point (OR = 2.71, 95% CI: 1.27–5.78), while the association on the right was of no statistical significance (OR = 1.01, 95% CI: 0.77–1.33). In summary, WWI was significantly associated with an increased likelihood of PAD in US adults, with a differential association between males and females.