Decision-making in musculoskeletal health care is complex, with discrepancy among clinical providers, and variation in the per cent of referrals for specialist care. To date there is an increased focus on specialist referrals, risking overuse of expensive testing and contributing to unnecessary treatment. This report will considerer the difficulties of primary care musculoskeletal decision-making using shoulder injuries as an example, presenting a solution based on multi-criteria decision-making analysis with online software. The associated issues involved in clinical decision-making are complex. Contributing to the components of complexity are; the aetiology of shoulders being multi-faceted, the experience and knowledge of providers, and the burden of patient demands. Notwithstanding, funding considerations, resource allocation availability, and other associated issues around clinical decision-making. Considering there are many facets involved in decision-making, this is an area where multi-criteria decision-making analysis (MCDM) may be appropriate. MCDM which uses mathematical analysis, is increasingly being used in health care and could be applied to the challenges of musculoskeletal care. MCDM has the potential to decrease variability in decision-making and be used as a tool to augment clinical decisions. Furthermore, the key clinical factors that decision-making is based on are to date unclear, therefore, this preliminary report offers a start towards moving to a clarification of the key factors, and an approach for implementing improved shoulder clinical care decision-making which could then be adapted and applied to other body sites.