Adaptation of liver to nutritional signals is regulated by several transcription factors that are modulated by intracellular metabolites. Here, we demonstrate a transcription factor network under the control of hepatocyte nuclear factor 4α (HNF4α) that coordinates the reciprocal expression of fatty acid transport and metabolizing enzymes during fasting and feeding conditions. Hes6 is identified as a novel HNF4α target, which in normally fed animals, together with HNF4α, maintains PPARγ expression at low levels and represses several PPARα-regulated genes. During fasting, Hes6 expression is diminished, and peroxisome proliferator-activated receptor α (PPARα) replaces the HNF4α/Hes6 complex on regulatory regions of target genes to activate transcription. Gene expression and promoter occupancy analyses confirmed that HNF4α is a direct activator of the Pparα gene in vivo and that its expression is subject to feedback regulation by PPARα and Hes6 proteins. These results establish the fundamental role of dynamic regulatory interactions between HNF4α, Hes6, PPARα, and PPARγ in the coordinated expression of genes involved in fatty acid transport and metabolism.