To maintain normal activity, single cells must assure that their energy needs and utilization are continuously matched. Likewise, multicellular organisms must constantly coordinate energy intake and expenditure to maintain energy homeostasis. The brain, and the hypothalamus in particular, plays a critical role in integrating and coordinating several types of signals, including hormones and nutrients, to guarantee such homeostasis. Like single cells, the hypothalamus also profits from intracellular pathways known to work as fuel sensors to maintain energy balance. One such pathway is the mammalian target of rapamycin (mTOR). mTOR integrates different sensory inputs to regulate protein synthesis rates in individual cells, and it has recently been implicated in the central nervous system to regulate food intake and body weight as well. This review provides an overview of the role of hypothalamic intracellular fuel sensors in the overall control of energy balance and discusses the potential contribution of these fuel-sensing mechanisms to the metabolic dysregulation associated with obesity.