Engaging in physical activity (PA) on a regular and adequate basis generates considerable benefits for health. In developed countries, the time spent doing PA is decreasing, whilst sedentary time (ST) is increasing. A multicomponent school-based intervention programme, called ‘Sigue la Huella’ (Follow the Footprint), was developed to reduce sedentary lifestyles and increase PA levels. This programme has proven to be effective in increasing the daily levels of moderate to vigorous PA, in decreasing ST and in improving motivational outcomes in secondary education students, in the city of Huesca (Spain). The study design was quasi-experimental, longitudinal and by cohorts, and it was carried out in four schools, two as an experimental group (n = 368) and two as a control group (n = 314). During the 25 months’ intervention, this programme adopted a holistic approach aiming to create favourable environments to engage in PA, and the empowerment of students to get actively involved in the design and execution of the activities, assuming responsibility for managing and optimizing their own PA. The programme is theoretically based on the social-ecological model and self-determination theory, and it provided evidence for four actions or components that can be used in school-based PA promotion: tutorial action, Physical Education at school, dissemination of information and participation in institutional programmes and events. The aim of this article is to describe the main characteristics of the intervention programme that have proved to be effective with respect to the objectives proposed.