Discrete emotions provide a lens for understanding students' subjective experiences in physical education (PE). Enjoyment of PE is one discrete emotion that receives a great deal of attention because it promotes students' interest and engagement. However, the implications of students' negative emotions toward PE remain less clear. Therefore, the purpose of this study was to examine relationships between students' negative emotions including shame, boredom, and anger in PE and self-reported disruptive behavior, leisure time moderate-to-vigorous physical activity (MVPA), and sedentary time. Middle school students (N = 401) completed surveys on all study variables seven weeks apart. Confirmatory factor analysis supported the validity and reliability of students' reports of negative emotions and behaviors across two time points. A cross-lagged design using structural equation modeling tested relationships between emotions and behavioral outcomes. Shame related to higher reports of future disruptive and sedentary behaviors and lower reports of leisure time MVPA. Boredom also related to lower reports of future leisure time MVPA. Lastly, anger related to higher reports of future disruptive behavior but lower reports of sedentary behavior. Each negative emotion produced unique relationship patterns that generally underscored undesirable student behaviors. Evaluating discrete emotions can highlight information regarding students' action tendencies. Understanding relationships between negative emotions and their resulting behaviors may help inform interventions and best teacher practices in PE. Overall, physical education teachers need to be aware of students' negative emotions and make pedagogical and content-related decisions to improve students' subjective experiences.