BACKGROUND: In 2014 the Danish Government introduced a wide-ranging school reform that applies to all public schools in Denmark. The reform involves changes in several aspects of the school structure and content. In a physical activity promotion perspective, a distinctive feature of the school reform is that it has become mandatory to integrate an average of 45 min of daily physical activity in the regular school day. The overarching objective of the PHASAR study is to evaluate the implementation and effect of this ambitious policy-driven physical activity promotion initiative on physical activity and overweight. This paper describes in detail the study protocol. METHODS: The evaluation is divided into a quantitative effect evaluation and a combined quantitative and qualitative process evaluation. A total of 31 schools are enrolled in the PHASAR study including more than 2,000 school-aged children. Objectively measured physical activity data are obtained in the PHASAR study in 2017/18 and compared to repeated cross sectional data collected in four historical school-based studies from 1998 to 2012. Body mass index data from 2012 to 2018 will be collected from The Child Database, which includes repeated cross-sectional assessments on approximately 100,000 children annually. In the absence of a control group, interrupted time-series analysis will be used to evaluate pre- and post-reform physical activity and body mass index levels and trends. A characterization of the school environment for physical activity promotion on a political, environmental, organizational and individual level and school implementation processes will be conducted to evaluate the implementation process. Data will be collected using interviews, surveys, document analyses and observations. DISCUSSION: The PHASAR study is a rare opportunity to evaluate the effectiveness of a nation-wide policy-driven school-based physical activity promotion initiative. The use of objectively measured pre- and post-reform physical activity and body mass index data combined with a characterization of the school implementation processes for physical activity promotion will provide a comprehensive source to evaluate the school reform. The study findings have the potential to influence national and international policy makers, health professionals and school staff.