Introduction Repetitive loading of the musculoskeletal system is suggested to be involved in the underlying mechanism of the majority of running-related injuries (RRIs). Accordingly, heavier runners are assumed to be at a higher risk of RRI. The cushioning system of modern running shoes is expected to protect runners again high impact forces, and therefore, RRI. However, the role of shoe cushioning in injury prevention remains unclear. The main aim of this study is to investigate the influence of shoe cushioning and body mass on RRI risk, while exploring simultaneously the association between running technique and RRI risk. Methods and analysis This double-blinded randomised controlled trial will involve about 800 healthy leisure-time runners. They will randomly receive one of two running shoe models that will differ in their cushioning properties (ie, stiffness) by ~35%. The participants will perform a running test on an instrumented treadmill at their preferred running speed at baseline. Then they will be followed up prospectively over a 6-month period, during which they will self-report all their sports activities as well as any injury in an internet-based database TIPPS (Training and Injury Prevention Platform for Sports). Cox regression analyses will be used to compare injury risk between the study groups and to investigate the association among training, biomechanical and anatomical risk factors, and injury risk. Ethics and dissemination The study was approved by the National Ethics Committee for Research (Ref: 201701/02 v1.1). Outcomes will be disseminated through publications in peer-reviewed journals, presentations at international conferences, as well as articles in popular magazines and on specialised websites.