Cirsium setidens is a perennial medicinal herb that is rich in flavonoids. We investigated in this study the effect of a C. setidens ethanol extract (CSE) on the development of nonalcoholic fatty liver in mice fed a high-fat diet (HF). C57BL/6J mice were fed either a control diet (CON) or HF for 8 weeks, and then fed CON, HF, or HF with 100 mg/kg of BW CSE (HF+CSE) for an additional 7 weeks. The final body weight and adipose tissue weight of the mice in the HF+CSE group were significantly lower than those in the HF group. CSE also markedly diminished both the lipid droplets in the liver tissues and decreased the hepatic and serum triglycerides (TG) concentrations. CSE strongly increased the hepatic mRNA levels of carnitine palmitoyltransferase (CPT1) and medium-chain acyl-CoA dehydrogenase (MCAD), the fatty acid β-oxidation enzymes. The hepatic levels of phosphorylated-AMP-activated protein kinase (AMPK) were significantly higher in the HF+CSF group than in the HF group. These results suggest that CSE inhibited hepatic fat accumulation by up-regulating the expression of the fatty acid β-oxidation genes.