This paper describes the design of the LIKE programme, which aims to tackle the complex problem of childhood overweight and obesity in 10–14-year-old adolescents using a systems dynamics and participatory approach. The LIKE programme focuses on the transition period from 10-years-old to teenager and was implemented in collaboration with the Amsterdam Healthy Weight Programme (AHWP) in Amsterdam-East, the Netherlands. The aim is to develop, implement and evaluate an integrated action programme at the levels of family, school, neighbourhood, health care and city. Following the principles of Participatory Action Research (PAR), we worked with our population and societal stakeholders as co-creators. Applying a system lens, we first obtained a dynamic picture of the pre-existing systems that shape adolescents’ behaviour relating to diet, physical activity, sleep and screen use. The subsequent action programme development was dynamic and adaptive, including quick actions focusing on system elements (quick evaluating, adapting and possibly catalysing further action) and more long-term actions focusing on system goals and/or paradigm change. The programme is supported by a developmental systems evaluation and the Intervention Level Framework, supplemented with routinely collected data on weight status and health behaviour change over a period of five years. In the coming years, we will report how this approach has worked to provide a robust understanding of the programme’s effectiveness within a complex dynamic system. In the meantime, we hope our study design serves as a source of inspiration for other public health intervention studies in complex systems.