The United Nations, through its 2030 Agenda and Sustainable Development Goals, advocates for the establishment of conducive environments for physical activity, following the ecological model. In line with this initiative, active transportation emerges as an accessible, cost-effective, and sustainable approach to augmenting daily physical activity levels. This study protocol endeavors to assess the impact of an active transportation education program rooted in the ecological model on the physical and mental well-being of high school students. Drawing upon scientific insights, we hypothesize that a 16-week active transportation intervention will lead to a 3% reduction in average body fat percentage and a noteworthy enhancement in executive function (including inhibition, cognitive flexibility, and working memory), physical fitness (comprising cardiorespiratory fitness and muscle strength), and mental health (encompassing mood disorders and cognitive functioning). If this intervention proves effective, it could offer a viable solution for the school community, especially in reducing congestion within the school environment. The study protocol aims to evaluate the impact of an active transportation educational program based on the ecological model on the physical and mental well-being of high school students. Three high schools located in the urban area of Talca, Chile, will be randomly selected (one public, one privately subsidized, and one private non-subsidized). Each high school will be randomly assigned an experimental group (n = 30) and a control group (n = 30; without intervention). The experimental groups will receive an active transportation educational intervention during their physical education classes for four months (60 to 90 min sessions, once a week), while the control group will receive no intervention. The primary outcome will provide information on body composition and executive function. Secondary outcomes will include objective physical activity level, physical fitness, mental well-being, academic achievement, health-related quality of life, perception of environmental urban features, physical activity barriers, and adherence to active transportation. It is expected that the results of the MOV-ES Project will transcend the physical health of schoolchildren and will have an impact on the school community, especially by decongesting the school environment.