Schools can enable students’ capability for lifelong physical activity (PA) by providing a physical, social and pedagogical context fostering students’ agency. This entails allowing them to develop their autonomy and ability to shape PAs according to what they value. This paper explores whether, and, if so, how, school practices provide the conditions for developing and employing PA-related student agency. We followed a multiple case study design, partnering with six secondary schools in the Netherlands. We based our qualitative content analysis on the schools’ policy documents and transcripts of interviews and focus groups with school management, teaching staff and supporting sports professionals. First, we analysed the space provided for PA-related student agency using the whole-of-school framework. Next, we used a social practice theory perspective to understand how each school practice allows for student agency. Results suggest that schools offer sufficient and varied PA opportunities but have not embedded deliberation with students on their meaningfulness and transfer to other contexts in their practices. We conclude that for schools to promote lifelong PA for students, there is a need for a pedagogical approach involving students’ perspectives, participation and reflections, enabling them to transfer PAs to other (future) life settings.