The hypothalamus is a brain region in charge of many vital functions. Among them, BAT thermogenesis represents an essential physiological function to maintain body temperature. In the metabolic context, it has now been established that energy expenditure attributed to BAT function can contribute to the energy balance in a substantial extent. Thus, therapeutic interest in this regard has increased in the last years and some studies have shown that BAT function in humans can make a real contribution to improve diabetes and obesity-associated diseases. Nevertheless, how the hypothalamus controls BAT activity is still not fully understood. Despite the fact that much has been known about the mechanisms that regulate BAT activity in recent years, and that the central regulation of thermogenesis offers a very promising target, many questions remain still unsolved. Among them, the possible human application of knowledge obtained from rodent studies, and drug administration strategies able to specifically target the hypothalamus. Here, we review the current knowledge of homeostatic regulation of BAT, including the molecular insights of brown adipocytes, its central control, and its implication in the development of obesity.