Fibrate drugs improve cardiovascular health by lowering plasma triglycerides, normalize low density lipoprotein levels, and raise high density lipoprotein (HDL) levels in patients with dyslipidemias. The HDL-raising effect of fibrates has been shown to be due in part to an increase in human apolipoprotein AI gene expression. However, it has recently been shown that fibrates can affect HDL metabolism in mouse by significantly decreasing hepatic levels of the HDL receptor scavenger receptor B-I (SR-BI) and the PDZ domain containing protein PDZK1. PDZK1 is essential for maintaining hepatic SR-BI levels. Therefore, decreased SR-BI might be secondary to decreased PDZK1, but the mechanism by which fibrates lower SR-BI has not been elucidated. Here we show that feeding PDZK1-deficient mice fenofibrate resulted in the near absence of SR-BI in liver, definitively demonstrating that the effect of fenofibrate on SR-BI is PDZK1-independent. Metabolic labeling experiments in primary hepatocytes from fenofibrate-fed mice demonstrated that fenofibrate enhanced the degradation of SR-BI in a post-endoplasmic reticulum compartment. Moreover, fenofibrate-induced degradation of SR-BI was independent of the proteasome, calpain protease, or the lysosome, and antioxidants did not inhibit fenofibrate-induced degradation of SR-BI. Using metabolic labeling coupled with cell surface biotinylation assays, fenofibrate did not inhibit SR-BI trafficking to the plasma membrane. Together, the data support a model in which fenofibrate enhances the degradation of SR-BI in a post-ER, post-plasma membrane compartment. The further elucidation of this novel degradation pathway may provide new insights into the physiological and pathophysiological regulation of hepatic SR-BI.