Physical education during long breaks is a crucial component of school physical education, ensuring one hour of daily physical activity within school. It plays an irreplaceable role in promoting students’ physical and mental health, enhancing their physical fitness, and cultivating good exercise habits. Relevant research in educational neuroscience suggests that exercise can maintain brain function and promote brain plasticity, making it the best investment for adolescent brains. However, traditional physical education during long breaks lacks fun and innovation, making it difficult for students to gain rich exercise experiences and cognitive benefits. Moreover, there are no clear standards for exercise load, and the effectiveness of these activities is often questioned. This case leverages educational neuroscience theories to analyze students’ learning situations, considering brain and physical development characteristics of junior high school students. It proposes some strategies such as optimizing activity content, creating exercise scenarios, and arranging exercise intensity appropriately. These strategies provide theoretical guidance and practical references for the design of junior high school physical education during long breaks, contributing to the innovation and development of school physical education programs.