The aim of this study was to investigate the protective effect of chlorogenic acid (CA) on liver injury caused by bile duct ligation (BDL), as well as the potential mechanism. Permanent bile duct ligation induced liver injury was evaluated by liver index, liver function and pathological observation. Oral administration of CA for 3 weeks markedly attenuated liver swelling and fibrosis. Blood biochemistry results revealed that CA decreased alanine transaminase, aspartate aminotransferase, alkaline phosphatase, total bilirubin, direct bilirubin and total bile acid. PCR analysis indicated that collagen I, collagen III, transforming growth factor and vascular endothelial growth factor mRNA were increased markedly by BDL treatment but these increases were suppressed by CA. Additionally, CA effectively alleviated the expression of α-smooth muscle actin induced by BDL. Taken together, our data indicate that CA can efficiently inhibit BDL-induced liver injury in rats, which is a candidate drug for preventing liver injury against cholestasis.