Whey protein is associated with improvement of metabolic syndrome. This study aimed to evaluate effects of whey protein on atherosclerosis in ApoE^−/− mice. Male ApoE^−/− mice were fed with a high-fat/cholesterol diet (HFCD), or HFCD supplemented with 10% or 20% whey protein for 18 wk. At the end of experiment, serum lipid profiles and inflammatory cytokines were assayed. Livers were examined using HE staining and Oil Red O staining. Aortas were used for en face and cryosection analyses to observe aortic lesions. Western blotting analysis was used to assess relative protein expression of cholesterol metabolism in the liver and aorta. No significant differences were observed in body weight or food intake among the three groups. Liver examination demonstrated decreased lipid droplets and cholesterol content in the whey-protein-supplemented groups. En face lesion of the aorta revealed a 21.51% and 31.78% lesion reduction in the HFCD supplemented with 10% and 20% whey groups, respectively. Decreased lesion was also observed in cryosection analysis. Whey protein significantly increased the serum high-density lipoprotein cholesterol level by 46.43% and 67.86%. The 20% whey protein significantly decreased serum IL-6 (a proinflammatory cytokine) by 70.99% and increased serum IL-10 (an anti-inflammatory cytokine) by 83.35%. Whey protein potently decreased lipogenic enzymes (ACC and FAS) in the liver and NF-κB expression in the liver and aorta. Whey protein significantly increased protein expression of two major cholesterol transporters (ABCA1 and ABCG1) in the liver and aorta. Thus, chronic whey protein supplementation can improve HFCD-induced atherosclerosis in ApoE null mice by regulating circulating lipid and inflammatory cytokines and increasing expressions of ABCA1 and ABCG1.