To evaluate the effectiveness of prefabricated foot orthoses for the prevention of lower limb overuse injuries in naval recruits.This study was a participant-blinded and assessor-blinded, parallel-group randomised controlled trial. Three-hundred and six participants aged 17-50 years who undertook 11 weeks of initial defence training at the Royal Australian Navy Recruit School (Cerberus, Australia) were randomised to a control group (flat insoles, n=153) or an intervention group (contoured, prefabricated foot orthoses, n=153). The combined incidence of medial tibial stress syndrome, patellofemoral pain, Achilles tendinopathy and plantar fasciitis/plantar heel pain during the 11-week training period were compared using incidence rate ratios (IRR). Data were analysed using the intention-to-treat principle.Sixty-seven injuries (21.9%) were recorded. The control and intervention group sustained 40 (26.1%) and 27 (17.6%) injuries, respectively (IRR 0.66, 95% CI 0.39 to 1.11, p=0.098). This corresponds to a 34% reduction in risk of developing medial tibial stress syndrome, patellofemoral pain, Achilles tendinopathy or plantar fasciitis/plantar heel for the intervention group compared with the control group. Participants in the prefabricated orthoses group were more likely to report at least one adverse event (20.3% vs 12.4%; relative risk (RR) 1.63, 95% CI 0.96 to 2.76; p=0.068; number needed to harm 13, 95% CI 6 to 253). The most common adverse events were foot blisters (n=20, 6.6%), arch pain (n=10, 3.3%) and shin pain (n=8, 2.6%).Prefabricated foot orthoses may be beneficial for reducing the incidence of lower limb injury in naval recruits undertaking defence training.Australian New Zealand Clinical Trials Registry: ACTRN12615000024549.