Changes in substrate utilization and reduced mitochondrial function following exposure to energy dense, high fat diets are putatively key components in the development of obesity related metabolic disease. Here we examined the effect of a 3-day high-fat diet (HFD) on isolated liver mitochondrial respiration and whole-body energy utilization in obesity prone (OP) rats. We also examined if hepatic overexpression (o/e) of peroxisomal proliferator-activated receptor co-activator-1α (PGC-1α), a master regulator of mitochondrial function and biogenesis would modify liver and whole body responses to the high fat diet. Acute, 3-day HFD (45% kcals) in OP rats resulted in increased daily energy intake, energy balance, weight gain, and adiposity; without producing increased liver triglyceride (TAG) accumulation. HFD fed OP rats also displayed decreased whole body substrate switching from the dark to light cycle which was paired with reductions in hepatic mitochondrial respiration of multiple substrates under multiple respiratory states. Hepatic PGC-1α o/e was observed to protect whole body substrate switching, as well as, maintaining mitochondrial respiration following the acute HFD. Additionally, liver PGC-1α o/e did not alter whole-body dietary fatty acid oxidation, but resulted in greater storage of dietary FFA in liver lipid, primarily as TAG. Together, these data demonstrate that short-term HFD can result in decreased metabolic flexibility and hepatic mitochondrial function in OP rats, which is completely prevented by hepatic overexpression of PGC-1α.