It is well-established that physical activity is beneficial to physical and psychological health. However, how physical activity contributes to psychological health is still unclear. In this investigation, we examined the association between physical activity and negative emotions assessed in real-time during simulated-peer-rejection. Moreover, we explored mediation of this association by higher-order neurocognitive functioning and cardiovascular flexibility. Although we found no evidence for mediation, we did find that greater physical activity predicted contextually responsive negative emotion. Specifically, greater physical activity predicted generation of negative emotions in response to peer-rejection and flexible reduction of negative emotions in response to peer-acceptance.