BACKGROUND: Overweight youngsters are better in absolute strength exercises than their normal-weight counterparts; a physiological phenomenon with promising psychological impact. In this paper we describe the study protocol of the Dutch, school-based program 'Focus on Strength' that aims to improve body composition of 11-13 year old students, and with that to ultimately improve their quality of life. METHODS: The development of this intervention is based on the Intervention Mapping (IM) protocol, which starts from a needs assessment, uses theory and empirical research to develop a detailed intervention plan, and anticipates program implementation and evaluation. This novel intervention targets first year students in preparatory secondary vocational education (11-13 years of age). Teachers are the program implementers. One part of the intervention involves a 30 % increase of strength exercises in the physical education lessons. The other part is based on Motivational Interviewing, promoting autonomous motivation of students to become more physically active outside school. Performance and change objectives are described for both teachers and students. The effectiveness of the intervention will be tested in a Randomized Controlled Trial in 9 Dutch high schools. DISCUSSION: Intervention Mapping is a useful framework for program planning a school-based program to improve body composition and motivation to exercise in 11-13 year old adolescents by a "Focus on Strength". TRIAL REGISTRATION: NTR5676 , registered 8 February 2016 (retrospectively registered).