There is an overwhelming agreement in scientific literature and global health guidelines that physical exercise is beneficial for health. Despite this, many people under-exercise, and instead choose to consume highly-palatable food (HPF) which is widely available in many societies. What neural mechanisms drive the prioritization of exercise, especially in the presence of HPF, remain unclear. We implement a novel paradigm allowing freely-behaving mice to choose between voluntary wheel-running and several other temptations. Mice displayed a clear preference to spending most of their time wheel-running without extrinsic reward, and maintained this preference even when HPF was included as a temptation. Causal and correlative analyses revealed that hypothalamic hypocretin/orexin neurons (HONs) instantiated the underlying appetitive (“approach”) and consummatory (“engagement”) psychological frameworks driving eating and exercising. The function of HONs is strongly context-dependent: HONs appear to promote decisions prioritizing exercise over feeding, rather than modulating either behavior in isolation. Using calcium photometry we confirm that natural HON fluctuations encode individual behavioral choices, displaying high activity during movement and rapid inhibition during feeding. Our data suggest a role for HONs in an eat-run arbitration maintaining exercise-behaviors in the presence of HPF.