Some studies have reported that the activation of peroxisome proliferator-activated receptor alpha (PPAR alpha) could protect against liver injury-induced by chemicals. In the present study, ultra-performance liquid chromatography coupled with electrospray ionization quadrupole mass spectrometry (UPLC-ESI-QTOFMS)-based metabolomics revealed the protective effects of PPARa activation by fenofibrate on LCA-induced liver injury, which recovered metabolic disorder of bile acids in the enterohepatic system. Fenofibrate treatment significantly promoted the biosynthesis of phospholipids via the upregulation of expression levels of phospholipase A(2) g6, g7, and g12b (Pla(2) g6, g7, and g12b) in liver, contributing to the decrease in hepatic transforming growth factor beta (TGF-beta) that regulates phospholipid homeostasis during liver injury. More importantly, the activation of PPARa by fenofibrate treatment protected against the enhanced expressions of the nuclear factor-kappa B (NF-kappa B) target genes, such as chemokine (C-C motif) ligand 2 (Ccl2) and secreted phosphoprotein 1 (Spp1). Its upstream factors related to NF-kappa B activation were also decreased by fenofibrate, including inflammasome, toll-like receptor (TLR), reactive oxygen species (ROS), and endoplasmic reticulum (ER) stress. Taken together, the current study demonstrated that PPARa activation could show a protective effect against LCA-induced liver injury using a metabolomics approach.