Seasonal obesity and fasting-associated hibernation are the two major metabolic events governing hepatic lipid metabolism in hibernating mammals. In this process, however, the role of the nuclear receptor known as peroxisome proliferator-activated receptor (PPAR)-α has not been elucidated yet. Here we show, as in human, that jerboa (Jaculus orientalis) liver expresses both active wild-type PPARα (PPARα1wt) and truncated PPARα forms and that the PPARα1wt to truncated PPARα2 ratio, which indicates the availability of active PPARα1wt, is differentially regulated during fasting-associated hibernation. Functional activation of hepatic jerboa PPARα, during prehibernating and hibernating states, was demonstrated by the induction of its target genes, which encode peroxisomal proteins such as acyl-CoA oxidase 1, peroxisomal membrane protein 70, and catalase, accompanied by a concomitant induction of PPARα thermogenic coactivator PPARγ coactivator-1α. Interestingly, sustained activation of PPARα by its hypolipidemic ligand, ciprofibrate, abrogates the adaptive fasting response of PPARα during prehibernation and overinduces its target genes, disrupting the prehibernation fattening process. In striking contrast, during fasting-associated hibernation, jerboas exhibit preferential up-regulation of hepatic peroxisomal fatty acid oxidation instead of the mitochondrial pathway, which is down-regulated. Taken together, our results strongly suggest that PPARα is subject to a hibernation-dependent splicing regulation in response to feeding-fasting conditions, which defines the activity of PPARα and the activation of its target genes during hibernation bouts of jerboas.Jerboa PPARα is subject to a hibernation-dependent splicing regulation in response to feeding-fasting conditions, which define activation of PPARα and its target genes.