Background: Running is one of the most popular and accessible physical activities in the world. However, running-related injuries are unfortunately very common. Scientific evidence is limited and scarce regarding (cost-)effectiveness and implementation process of interventions for running-related injuries prevention. Thus, the objective of this study will be to investigate the effectiveness, cost-effectiveness and implementation process of a running-related injury prevention program (RunIn3). Methods: This is the protocol of a pragmatic hybrid type 1 randomized controlled trial. There will be 530 runners over 18 years old, without running-related injuries in the last 3 months from São Paulo, Brazil. This program will be delivered online with two broad actions: (1) to provide feedback on individual training characteristics and running-related injury risk; and (2) providing/enhancing knowledge, skills and self-efficacy on running-related injury preventive behaviors. The primary outcome will be the proportion of runners reporting running-related injuries. The secondary outcomes will be preventive behaviors, direct and indirect costs, and implementation outcomes. The main effectiveness analysis on the primary outcome will be performed using linear probability mixed models in order to allow outcome changes over time and to yield the absolute risk reduction between-groups. Discussion: The main hypothesis of this study is that the RunIn3 program will be effective in reducing the running-related injury risk and in promoting preventive behavior, either by increasing the frequency of healthy behaviors or by reducing the frequency of risk behaviors. Moreover, if the RunIn3 program is effective in reducing the running-related injuries risk, we believe that this effect would go alongside with a reduction of societal costs. Trail registration: Clinicaltrials.gov (NCT03892239) Registered 5 February 2019 - Prospectively registered, https://clinicaltrials.gov/ct2/show/NCT03892239.