Foot orthoses are one of the most used strategies by healthy runners in injury prevention and performance improvement. However, their effect on running kinematics throughout an intense prolonged run in this population is unknown. Moreover, there is some controversy regarding the use of custom-made versus prefabricated foot orthoses. This study analysed the effect of different foot orthoses (custom-made, prefabricated and a control condition) on spatio-temporal and angular (knee flexion and foot eversion) kinematic parameters and their behaviour during an intense prolonged run. Twenty-four recreational runners performed three similar tests that consisted of running 20 min on a treadmill at 80% of their maximal aerobic speed, each one with a different foot orthosis condition. Contact and flight time, and stride length and stride rate were measured every 5 min by an optical measurement photoelectric cell system. Knee flexion and foot eversion kinematic parameters were measured by two high-speed cameras. No significant differences were found between the different foot orthoses in any of the time points studied and between the interaction of foot orthosis and behaviour over time, in any of the variables studied (P > 0.05). The use of custom-made and prefabricated foot orthoses during an intense prolonged run does not produce changes in spatio-temporal and kinematic parameters in healthy runners. These results suggest that a healthy runner maintains its ideal movement pattern throughout a 20 minute prolonged run, regardless the type of foot orthosis used.