<p>Fenofibrate, a peroxisome proliferator-activated receptor α (PPARα) agonist, is widely prescribed to treat hyperlipidemia and has therapeutic potential in liver and kidney diseases. However, fenofibrate is also associated with adverse effects, including elevated creatinine and liver and kidney toxicity, although the underlying mechanisms remain unclear. In addition, how fenofibrate regulates lipid metabolism differently in the liver and kidney is not well understood. Therefore, in this study, we investigated the dose-dependent effects of fenofibrate on liver and kidney metabolism in rats, with a focus on PPARα activation and potential mechanisms contributing to organ-specific toxicity. We used high-throughput transcriptomic data from 5-day rat in vivo studies, where rats were exposed to fenofibrate, and performed pathway enrichment, injury module, and detailed individual gene comparison analyses to investigate how liver and kidney metabolism were differentially altered between the two organs. Fenofibrate exposure significantly increased liver but not kidney weights and caused larger perturbations in the liver compared to the kidney transcriptome, with the majority of the changes related to PPARα regulation. Interestingly, our study revealed that the <i>PPARα</i> and <i>RXRα</i> genes are differentially regulated between the liver and kidney. In addition, we identified several differences between them in cellular and mitochondrial fatty acid transport, lipoprotein metabolism, fatty acid oxidation, branched-chain amino acid degradation, and glucose metabolism pathways. Furthermore, we identified transcriptomic inflection points at which the changes in the PPARα-mediated regulation of lipid metabolism switched from beneficial to deleterious as the fenofibrate concentration increased leading to liver injury, providing potential mechanisms of toxicity.</p>