Objectives Recurrent ankle sprains can be reduced by a neuromuscular training program (NMT). The way NMT is delivered may influence the incidence of long term recurrent injuries, residual pain and disability. Design This RCT with a follow-up of twelve months, evaluated whether the implementation method of a proven effective NMT program delivered by a mobile application or a written instruction booklet, resulted in differences in injury incidence rates, functional ankle disability/pain in the long term, assuming equal compliance – as is shown in previous research – with the 8-week intervention. Methods 220 athletes with a history of ankle sprain were recruited for this RCT. 110 athletes were offered the freely available “Strengthen your ankle App” and the other 110 received a printed Booklet. Primary outcome measure was incidence density of ankle sprains. Secondary outcome measures were residual pain/disability and the individual cumulative number of ankle sprains during follow-up. Results The incidence densities of self-reported ankle sprain recurrences were not significantly different between both groups (HR 1.06; 95% CI 0.76–1.49). Median FADI (Functional Ankle and Disability Index) scores increased equally over time in both groups, indicating a lower rate of limitation and pain in both groups at follow-up. Neither FADI scores nor cumulative recurrent injuries were significantly different between groups. Conclusions This study showed that the implementation method of a NMT program by using an App or a Booklet did neither lead to different injury incidence rates in the long term nor did it influence residual functional disability/pain. Assuming equal compliance during the 8-week intervention, both methods show similar effectiveness in twelve-month follow-up.