Berberine (BBR), one of the main bioactive compounds in Rhizoma coptidis, has multiple pharmacological activities. It has been reported that 8-cetylberberine (8-BBR-C16) has increased anti-microbial property in vivo and a higher bioavailability in hamsters. Therefore, in the present study, we used apolipoprotein E-deficient mice (ApoE−/−) as an atherosclerosis model to investigate the anti-atherosclerosis effects of 8-BBR-C16. After 12 weeks of treatment, the atherosclerotic plaque area of the aorta, serum lipid profile, the plasma redox state and the expression of inflammatory cytokines in ApoE−/− mice were determined. Both BBR and 8-BBR-C16 significantly decreased the atherosclerotic plaque area by suppressing inflammatory and oxidative markers in ApoE−/− mice. Treatment with BBR or 8-BBR-C16, decreased serum levels of IL-1β and TNF-α as well as mRNA levels of NF-κBp65, i-NOS, ICAM-1, IL-6 in the aorta. In addition, the expression of NF-κB p65 protein decreased in the nucleus, whereas IκBα levels increased in the cytosol. The anti-inflammatory and anti-oxidative effect of BBR and 8-BBR-C16 attributed to inhibition of the translocation of NF-κB to the nucleus. Since the dosage of BBR used was 10 fold higher than that of 8-cetylberberine, we conclude that 8-BBR-C16 is more efficient in treating atherosclerosis in ApoE−/− mice.