Puerariae flower extract (PFE) is a crude extract of the Kudzu flower. Previous studies have shown that PFE supplementation exerts anti-obesity and anti-fatty liver effects in high-fat diet-fed mice. In this study, we aimed to identify the PFE components responsible for these effects and to determine their influence on energy expenditure and uncoupling protein 1 (UCP1) expression. Experiments were conducted on C57BL/6J male mice classified into 3 groups: (1) high-fat diet-fed (HFD), (2) high-fat diet-fed given PFE (HFD + PFE), and (3) high-fat diet-fed given the PFE isoflavone-rich fraction (HFD + ISOF). All groups were fed for 42 days. The HFD + PFE and HFD + ISOF groups showed significant resistance to increases in body weight, hepatic triglyceride level, and visceral fat compared to the HFD group. These groups also exhibited significant increases in oxygen consumption and UCP1-positive brown adipose tissue (BAT) area. Our results demonstrate that the active ingredients in PFE are present in the ISOF and that these compounds may increase energy expenditure by upregulation of BAT UCP1 expression. These findings provide valuable information regarding the anti-obesity effects of isoflavones.