Neurons in both the orbitofrontal cortex (OFC) and medial frontal cortex (MFC) encode the sensory properties, magnitude and subjective value of expected and received rewarding outcomes. In addition, the activity of neurons in these regions reflects anticipatory arousal, as measured by pupil diameter. Decision-making and representations of arousal are intimately linked. How these processes interact at the level of single neurons as well as neural circuits are unknown. To understand how OFC and MFC influence arousal and decision making, we recorded neural activity from both regions while animals made reward-guided decisions. Heart rate (HR) was recorded as a proxy for arousal. In intact animals we found that higher HR facilitated reaction times (RTs). Concurrently, a set of neurons in OFC and MFC selectively encoded trial-by-trial variations in HR independent of reward magnitude. After amygdala lesions, HR generally increased and the relationship between HR and RTs was reversed. Concurrent with this change, there was an increase in the proportion of MFC neurons encoding HR. At the population level, the balance of encoding in MFC shifted towards signaling HR, suggesting a specific mechanism through which arousal influences decision-making.