Cooperation is crucial in classrooms for positive interactions among pupils, but the factors influencing children's cooperative behaviors remain debated. This study explores the impact of cardiac vagal tone (CVT), a measure of physiological self-regulation, and cognitive control on cooperation among 109 primary school students. Heart rate variability was used to assess self-regulation, and cognitive control was evaluated through an AX-Continuous Performance Task. Cooperative behavior was measured with a child-friendly Stag Hunt game. Results showed that moderate CVT is related to increased cooperative actions, but no direct relationship between cognitive control types and cooperation was found. However, an interaction effect indicated that moderate CVT particularly boosts cooperation in children who employ proactive cognitive control. These findings emphasize the need to develop physiological self-regulation skills to enhance cooperative behavior in educational settings, supporting better social, and emotional well-being, and learning outcomes.