Lithospermum erythrorhizon, which has traditionally been used as a vegetable and to make the liquor Jindo Hongju, contains several naphthoquinone pigments, including shikonin. This study aimed to evaluate the antiobesity effects of Lithospermum erythrorhizon ethanol extract (LE) and elucidate the underlying mechanism. C57BL/6J mice were fed a normal or high-fat diet with or without LE supplementation for 8 weeks. LE reduced high-fat diet-induced increases in body weight, white adipose tissue mass, serum triglyceride and total cholesterol levels, and hepatic lipid levels while decreasing lipogenic and adipogenic gene expression. Furthermore, acetylshikonin suppressed adipocyte differentiation in a dose-dependent manner and significantly attenuated adipogenic transcription factor expression in 3T3-L1 cells. These findings suggest that Lithospermum erythrorhizon prevents obesity by inhibiting adipogenesis through downregulation of genes involved in the adipogenesis pathway and may be a useful dietary supplement for the prevention of obesity.