INTRODUCTION: The theory of human functioning and school organization proposes that schools promote health by strengthening students' educational engagement. Previous studies have relied on proxy measures of engagement and not examined sexual health. This paper addresses these gaps. METHODS: Longitudinal data came from the control arm of a randomized trial involving female and male students ages 12-14 in English secondary-schools (n = 3337 students). Exposures measured at baseline included a proxy measure of school-level engagement (value-added education, VAE: the difference between observed absence and attainment rates and those predicted based on student characteristics) and direct measures of school- and student-level engagement (commitment, belonging, relationships and participation). Sexual behavior was measured at 24- and 36-months, including sexual debut and contraception use at first sex. RESULTS: Higher school-level VAE was associated with an increased risk of early sexual debut at 24-months. Students attending schools with higher overall levels of commitment and belonging were less likely to report sexual debut at 36 months. Students reporting stronger personal commitment to learning and teacher relationships at baseline were less likely to report sexual debut at both follow-up points. Associations involving participation and contraception use were largely nonsignificant. CONCLUSIONS: Direct measures of the school environment are more strongly associated with reduced sexual risk behavior in early adolescence than the proxy measure, VAE. Results provide some support for the theory and suggest that personal disposition towards school as well as attending a school with high levels of student commitment and belonging are important for subsequent sexual decision making.