Pexidartinib is a regulatory agency approved small molecule kinase inhibitor (KI) with a boxed warning for hepatotoxicity, and FDA requires a Risk Evaluation and Mitigation Strategy (REMS) to mitigate such risk. The mechanism of pexidartinib hepatotoxicity is poorly understood. As mitochondrial injury and hepatocyte toxicity have been proposed to be a shared mechanism for the hepatotoxicity induced by many KIs, here we examined pexidartinib for such liabilities. Freshly isolated rat liver mitochondria, submitochondrial fractions, and cryopreserved primary human hepatocytes (PHHs) - the gold standard in vitro model for drug hepatotoxicity - were treated with pexidartinib at clinically relevant concentrations, and mitochondrial functions and cytotoxicity were assessed. In isolated mitochondria, the state 3 oxygen consumption rates of glutamate/malate- and succinate-driven respiration were both decreased by pexidartinib, while the state 4 oxygen consumption rates were unaffected. In submitochondrial fractions, the activities of respiratory chain complex (RCC) I and V, but not II, III, IV, were significantly inhibited by pexidartinib. In PHHs, as measured by a Seahorse system, pexidartinib decreased basal, spare, maximal, and adenosine triphosphate (ATP)-linked respirations at 2 h in the absence of cell death. Pexidartinib also inhibited cellular ATP level, increased reactive oxygen species, and caused cell death after 24 h. However, activities of caspases were unaffected. Importantly, the detrimental effects noted above occurred at pexidartinib concentrations of 0.5- to 2.5-fold of the human peak blood concentration (Cmax) achieved with the recommended therapeutic dose. These data suggest that mitochondrial injury and hepatocyte toxicity are involved in the mechanism of pexidartinib-induced hepatotoxicity.