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Recognition of the importance and value of collaboration and involving stakeholders throughout the research process has given rise to the establishment of the Welsh Institute for Physical Activity, Health and Sport (WIPAHS). Globally, formal collaborations between researchers and stakeholders to complete research projects, remains insufficient. Therefore, the primary aim of WIPAHS is to engage in long-term, forward-thinking collaborations that address practice-informed research questions, to disseminate findings widely, and translate them into practice and policy. This study explored the implementation and subsequent refinement of a national institute for physical activity, health, and sport. Through a qualitative exploratory design, thirteen, individual, semi-structured, online interviews were conducted with academic members of the WIPAHS Research Steering Group. The data were thematically analysed by the research team to identify themes and subsequently used to formulate a set of Principles of Working. Fifteen sub-themes were generated which led to eight Principles of Working emphasising national unity and the commitment to working collaboratively across all of Wales, UK, for the benefit of Wales. The role of collaboration in amplifying real-world impact was particularly highlighted; collaborative efforts between academics and stakeholders, underpinned by a clear structure and equal opportunities, were believed to facilitate a reduction in research duplication and optimal efficiency. Formalising the developmental process and the resulting Principles of Working provides a replicable blueprint for other academics to consider creating similar national institutes. This approach enables co-ordinated, systems-wide efforts to promote and advance health-enhancing physical activity and sport, offering a model for others seeking a comprehensive approach to achieve these goals.