Background Running-related injuries (RRIs) can be considered the primary enemy of runners. Most literature on injury prediction and prevention overlooks the mental aspects of overtraining and under-recovery, despite their potential role in injury prediction and prevention. Consequently, knowledge on the role of mental aspects in RRIs is lacking. Objective To investigate mental aspects of overtraining and under-recovery by means of an online injury prevention programme. Methods and analysis The € Take a Mental Break!' study is a randomised controlled trial with a 12 month follow-up. After completing a web-based baseline survey, half and full marathon runners were randomly assigned to the intervention group or the control group. Participants of the intervention group obtained access to an online injury prevention programme, consisting of a running-related smartphone application. This app provided the participants of the intervention group with information on how to prevent overtraining and RRIs with special attention to mental aspects. The primary outcome measure is any self-reported RRI over the past 12 months. Secondary outcome measures include vigour, fatigue, sleep and perceived running performance. Regression analysis will be conducted to investigate whether the injury prevention programme has led to a lower prevalence of RRIs, better health and improved perceived running performance. Ethics and dissemination The Medical Ethics Committee of the University Medical Center Utrecht, the Netherlands, has exempted the current study from ethical approval (reference number: NL64342.041.17). Results of the study will be communicated through scientific articles in peer-reviewed journals, scientific reports and presentations on scientific conferences.