Organismal energy homeostasis is maintained by complex interorgan communications making the discovery of novel drugs against metabolic diseases challenging using traditional high-throughput approaches in vitro. Here, we describe a method that rapidly identifies small molecules with an impact on organismal energy balance in vivo. Specifically, we developed a whole-organism screen for modulators of fasting metabolism using transgenic bioluminescence-reporter zebrafish for the gluconeogenic gene phosphoenolpyruvate-carboxykinase 1 (pck1).