The effects of footwear on the walking kinematics, kinetics and electromyography (EMG) of individuals with chronic ankle instability (CAI) at different speeds are still unknown. The objective of this cross-sectional study was to evaluate the kinematic, kinetic and electromyography differences between shod and barefoot walking at comfortable (CW) and fast (FW) speeds in individuals with CAI. Twenty-one individuals with CAI walked on a 5-meter walkway shod and barefoot at CW and FW speeds. A force plate was used to record the ground reaction forces, a 3-D motion analysis system to record the lower limb kinematics and a surface EMG system to collect the gluteus medius, vastus lateralis, gastrocnemius lateralis, gastrocnemius medialis, peroneus longus and tibialis anterior muscles activity. The dependent variables were ankle and knee angles and moments and normalized muscle activity. The shod and barefoot data during CW and FW were compared using a one-dimensional non-parametric mapping analysis. The main results of this study were that individuals with CAI exhibited more ankle dorsiflexion angle, knee extension and tibialis anterior muscle activation during the beginning of the stance phase during shod compared to barefoot walking. Also, the biomechanical effects of shoes are similar during walking at FW and CW. The biomechanical deficits associated with CAI were partly attenuated during the shod compared to the barefoot condition and these effects were similar at CW and FW. These findings are compatible with the concept that locomotor interventions using suitable shoes may enhance gait abilities in individuals with CAI.