Evidence shows that regular physical activity is enhanced by supporting environment. Studies are needed to integrate research evidence into health enhancing, cross-sector physical activity (HEPA) policy making. This article presents the rationale, study design, measurement procedures and the initial results of the first phase of six European countries in a five-year research project (2011–2016), REsearch into POlicy to enhance Physical Activity (REPOPA). REPOPA is programmatic research; it consists of linked studies; the first phase studied the use of evidence in 21 policies in implementation to learn more in depth from the policy making process and carried out 86 qualitative stakeholder interviews. The second, ongoing phase builds on the central findings of the first phase in each country; it consists of two sets of interventions: game simulations to study cross-sector collaboration and organizational change processes in the use of evidence and locally tailored interventions to increase knowledge integration. The results of the first two study phases will be tested and validated among policy makers and other stakeholders in the third phase using a Delphi process. Initial results from the first project phase showed the lack of explicit evidence use in HEPA policy making. Facilitators and barriers of the evidence use were the availability of institutional resources and support but also networking between researchers and policy makers. REPOPA will increase understanding use of research evidence in different contexts; develop guidance and tools and establish sustainable structures such as networks and platforms between academics and policy makers across relevant sectors.