The hypothalamus plays a crucial role in the regulation of food intake and energy expenditure. One of the main regulatory factors within the hypothalamus is AMP-activated protein kinase (AMPK), which is involved in a large number of biological actions including the modulation of energy balance. Leptin and ghrelin-induced changes in hypothalamic AMPK lead to important alterations in hypothalamic fatty acid metabolism. Furthermore, it is well known that the hypothalamus controls peripheral lipid metabolism through the sympathetic nervous system, and those actions are independent of food intake. In this short review, we highlight the main molecular pathways triggered by leptin and ghrelin altering both central and peripheral lipid metabolism and, therefore, controlling feeding behavior and energy expenditure.