BACKGROUND: The aim of the study; LCoMotion - Learning, Cognition and Motion was to develop, document, and evaluate a multi-component physical activity (PA) intervention in public schools in Denmark. The primary outcome was cognitive function. Secondary outcomes were academic skills, body composition, aerobic fitness and PA. The primary aim of the present paper was to describe the rationale, design and methods of the LCoMotion study. METHODS/DESIGN: LCoMotion was designed as a cluster-randomized controlled study. Fourteen schools from all five regions in Denmark participated. All students from 6th and 7th grades were invited to participate (n = 869) and consent was obtained for 87% (n = 759). Baseline measurements were obtained in November/December 2013 and follow-up measurements in May/June 2014. The intervention lasted five months and consisted of a "package" of three main components: PA during academic lessons, PA during recess and PA homework. Furthermore a cycling campaign was conducted during the intervention period. Intervention schools should endeavor to ensure that students were physically active for at least 60 min every school day. Cognitive function was measured by a modified Eriksen flanker task and academic skills by a custom made mathematics test. PA was objectively measured by accelerometers (ActiGraph, GT3X and GT3X+) and aerobic fitness assessed by an intermittent shuttle-run test (the Andersen intermittent running test). Furthermore, compliance with the intervention was assessed by short message service (SMS)-tracking and questionnaires were delivered to students, parents and teachers. DISCUSSION: LCoMotion has ability to provide new insights on the effectiveness of a multicomponent intervention on cognitive function and academic skills in 6th and 7th grade students. TRIAL REGISTRATION: Clinicaltrials.gov: NCT02012881 (10/10/2013).