Fucoxanthin, a characteristic carotenoid of brown algae, has been reported to exert an anti-diabetic effect in an obese murine model. Wakame (Undaria pinnatifida), an edible seaweed, is rich in fucoxanthin. This study examined the anti-obesity and anti-diabetic effects of fucoxanthin-rich wakame lipids (WLs) on high fat (HF) diet-induced obesity in mice. Mice were fed a high fat control (HFC) or normal fat control (NFC) diet for 10 weeks. The HF diet-fed group was administered a HF diet containing WLs for a further 5 weeks. Parameters related to diabetes and obesity conditions were evaluated and compared. The HF-WL diet, which was rich in fucoxanthin, significantly suppressed body weight and white adipose tissue (WAT) weight gain induced by the HF diet. Dietary administration of the HF diet resulted in hyperglycemia, hyperinsulinemia and hyperleptinemia in the mouse model. These perturbations were completely normalized in the HF-WL diet-fed group. Increased expression of monocyte chemoattractant protein-1 (MCP-1) mRNA expression was observed in HFC mice, but was normalized in the HF-WL groups. Moreover, the HF-WL diet promoted mRNA expression of β3-adrenergic receptor (Adrb3) in WAT and glucose transporter 4 (GLUT4) mRNA in skeletal muscle tissues. These results suggest that dietary WLs may ameliorate alterations in lipid metabolism and insulin resistance induced by a HF diet. There is therefore a biochemical and nutritional basis for the application of fucoxanthin-rich WLs as a functional food to prevent obesity and diabetes-related disorders.