This paper examines how children's agency operates within primary education in England through an in-depth qualitative study of three contrasting schools over two years. While children's right to participate in decisions affecting their education is increasingly recognised internationally, its practical implementation within formal education systems remains challenging. Drawing on critical realism and extensive empirical evidence, including classroom observations, interviews with school leadership and teachers, and innovative participatory methods capturing children's own voices, this study reveals how different institutional approaches create varying opportunities for children's agency. Through analysing structural conditions, daily practices, and children's experiences across two academic years, the research demonstrates how agency emerges through complex interactions between educational structures and children's lived experiences. The findings reveal that supporting children's agency does not require choosing between agency and structure; rather, thoughtfully designed structures can enable meaningful participation while maintaining educational standards. The paper presents the concept of 'structured freedom'--a practical framework for systematically supporting children's agency through four key principles: three-domain integration, choice architecture, systematic mechanisms for agency, and experiential development. This study offers both theoretical insights into how children's agency operates within educational structures and practical guidance for schools navigating the tensions between enabling children's agency and meeting standardised requirements.