The principal substrate used by the normal adult human heart is free fatty acids, the remainder being, predominantly, carbohydrate. During failure, the heart becomes less reliant on fatty acid metabolism, possibly as a result of tissue hypoxia. Therefore, understanding hypoxic adaptation may explain the metabolic changes that occur during the development of heart failure and potential therapeutic advancement. As peroxisome proliferator activated receptor alpha (PPARα) modulates cardiac fatty acid metabolism, we investigated the role of PPARα in cardiac metabolic adaptation to chronic hypoxia. We have reported isolated hearts from chronically hypoxic (11% O2 for 3 weeks) mice were more glycolytic, had reduced PPARα expression and decreased fatty acid metabolism, but had normal function, determined using in vivo cine-MRI. 31P MRS of isolated perfused mouse hearts showed a drop in phosphocreatine (PCr) with hypoxia, but ΔGATP was not altered, indicating that metabolic reprogramming was sufficient to maintain ATP production and contractile function. Increased or decreased PPARα expression, using a high fat diet or PPARα null mice, respectively, prevented metabolic adaptation to hypoxia and caused cardiac dysfunction. Cardiac vascular endothelial growth factor (VEGF), prominent hypoxia-inducible factor (HIF) target, was increased by hypoxia, indicating that HIF may have been involved in metabolic adaption. In order to determine the relationship between HIF and PPARα, HIF was stabilised pharmacologically using FG2216/BIC in HL-1 cardiomyocytes, to show decreased PPARα expression and caused similar metabolic changes to those seen in the in vivo hypoxic heart. We proposed that HIF-mediated downregulation of PPARα is crucial for metabolic adaptation and maintenance of cardiac function during chronic hypoxia.