PURPOSE: Chronic ankle instability (CAI) alters lower extremity neuromuscular function, associated with a change in corticomotor excitability. The aim of this study was to compare corticomotor excitability and neuromuscular function of the muscles around the ankle between athletes with CAI and without CAI (non-CAI). METHODS: Nineteen CAI athletes (15 men and 4 women) and 19 non-CAI athletes (15 men and 4 women) participated (age- and sex-matched). Corticomotor excitability was measured by transcranial magnetic stimulation for the following muscles: the tibialis anterior (TA), peroneus longus (PL) and gastrocnemius medialis (GM). The resting motor threshold (rMT), motor evoked potential (MEP), and latency (Lat) were subsequently measured. Neuromuscular function was assessed with a jump test, using the EMG activity before foot contact, peak torque, and joint position sense. RESULTS: The corticomotor excitability in CAI showed a lower normalized MEP in the TA (p = 0.026) and PL (p = 0.003), and longer latency in the TA (p = 0.049) and GM (p = 0.027) compared with non-CAI. The neuromuscular assessment showed CAI had less EMG activity of the PL (p < 0.001), less peak torque of the dorsiflexor (p = 0.019) muscle compared with non-CAI. CONCLUSION: Athletes with CAI had lower corticomotor excitability in the TA and PL and a longer latency in the TA and GM muscles. Additionally, CAI demonstrated functional neuromuscular deficits by decreasing EMG activity of the PL muscle and strength of the dorsiflexor muscle. Our findings indicated maladaptation at both cortical and peripheral levels among athletes with CAI.