Objectives The aim of this study was to examine the effectiveness of an enhanced online injury prevention programme on the number of running-related injuries (RRIs) in recreational runners. Methods We conducted a randomised-controlled trial in runners who registered for running events (distances: 10–42.195 km) in the Netherlands. Adult runners who provided informed consent were randomised into the intervention or control group. Participants in the intervention group received access to the online prevention programme, which included items to prevent RRIs. Participants in the control group followed their regular preparation for the running event. The primary outcome measure was the number of new RRIs from baseline to 1 month after the running event. To determine differences between injury proportions, univariate and multivariate logistic regression analyses were performed. Results This study included 4050 recreational runners (63.5% males; mean (SD) age: 42.3 (12.1) years) for analyses. During follow-up, 35.5% (95% CI: 33.5 to 37.6) of the participants in the intervention group sustained a new RRI compared with 35.4% (95% CI: 33.3 to 37.5) of the participants in the control group, with no between-group difference (OR: 1.03; 95% CI: 0.90 to 1.17). There was a positive association between the number of items followed in the injury prevention programme and the number of RRIs (OR: 1.05; 95% CI: 1.00 to 1.11). Conclusion The enhanced online injury prevention programme had no effect on the number of RRIs in recreational runners, and being compliant with the programme paradoxically was associated with a slightly higher injury rate. Future studies should focus on individual targeted prevention with emphasis on the timing and application of preventive measures.