© 2019 by the authors. Licensee MDPI, Basel, Switzerland. Taking part in regular physical activity (PA) is important for young adolescents to maintain physical, social and mental health. Schools are vibrant settings for health promotion and the complexity of driving a whole-school approach to PA has not been tested in the Irish school context. The feasibility of the pilot programme of the Department of Education and Skills second level Active School Flag (SLASF) is needed. SLASF is a two year process that consists of the Active School Flag (ASF) certificate programme (year 1) and the ASF flag programme (year 2). This protocol paper is specific to the first year certificate process. Three schools around Ireland were recruited as pilot schools to carry out the year-long SLASF programme with 17 planned actions involving the entire school. Students in the transition year programme have a particular role in the promotion of PA in SLASF. Data collection consists of physical measures, accelerometers, survey data and interviews at the beginning and the end of the academic year. The primary focus on the feasibility of the programme is through process evaluation tools and fidelity checks consisting of implementation of the SLASF programme through whole-school surveys, focus group discussions of key stakeholder groups, as well as one-to-one interviews with a member of management at each school and the SLASF coordinator of the school. Secondary outcomes include PA levels and its social cognitive theories based correlates through physical health measures, surveys carried out pre- and post-intervention, as well as focus group discussions of the students. The results of this study are needed to improve the development of the SLASF through a predetermined stopping criteria and inclusion into systems thinking approaches such as the Healthy Ireland Demonstration Project.