Background Cross-sectoral collaborations are considered necessary to address detrimental health, social, educational and economic outcomes that impact marginalised and disadvantaged populations. There is a strong relationship between the health of children and their educational attainment; good health promotes positive learning. This paper reports cross-sectoral executive and senior management level systems changes required to enable the design of a collaborative primary healthcare service model for children and young people in rural Australia. Methods A descriptive qualitative design was used. Data were collected from executive and senior managers from three organisations (Education, Health and a University Department of Rural Health [n = 6]) through individual semi-structured interviews. Data were analysed using an inductive, thematic approach. The study draws on Lewin’s Model of Change. Results Three overarching themes were generated from the data: an embedded challenge and experimental solutions; building a shared language and understanding; and the role of relationships and trust. Despite the unique geographical and social context of the study area, strategies emerged from the data on how a solution to an embedded challenge, through design of a primary healthcare model, was established and how the strategies described could be transferred and scaled to other rural and remote communities. Conclusion Contextual differences make each rural and remote area unique. In this study, strategies that are described in the managing change literature were evident. The authors conclude that drawing on strong management of change principles could mean that a service model designed for one remote community might be transferrable to other communities.