Lower limb overuse injuries are common among people who are exposed to physical stress. Orthotic shoe insoles are widely used to prevent lower limb overuse injuries. Here, we conducted a randomized-controlled study to examine whether the use of orthotic insoles prevents lower limb overuse injuries. Participants (n=228) were randomly assigned to use (n=73) or not to use (n=147) orthotic insoles. The insoles were molded to the shape of the foot to provide support during physical activity. The main outcome measure in the present study was the physician-diagnosed lower limb overuse injury. Thirty-four (46.6%) subjects in the insole group were diagnosed with a lower limb overuse injury compared with 56 (38.1%) in the control group (P=0.29) during the 6-month study period. When body mass index and the results of a 12-min running test and muscle strength were adjusted in a Cox's regression model, the hazard ratio for lower limb overuse injury in the insole group was 1.3 (95% confidence intervals: 0.8–2.1) compared with the control group. Use of orthotic insoles was not associated with a decrease in lower limb overuse injuries. Our findings suggest that routine use of orthotic insoles does not prevent physical-stress-related lower limb injuries in healthy young male adults.