The pparab subtype in zebrafish is much more highly expressed in tissues with high oxidative activity than pparaa. r The pparab deficiency in zebrafish reduces fatty acid β-oxidation both in liver and muscle, illustrating its functional homology as a mammalian peroxisome proliferator-activated receptor α (PPARα). r pparab deficiency promotes metabolic reprogramming by increasing glucose utilization and inhibiting amino acid breakdown. r The present study brings new insights into the comprehensive regulatory roles of PPARα in the cellular fuel selection and provides a valuable animal model for PPARα studies from a viewpoint of comparative physiology.