The purpose of this study was to compare alterations in peroneal latency and electromechanical delay (EMD) following an inversion perturbation during walking in patients with functional ankle instability (FAI) and with a matched control group. Peroneal latency and EMD were measured from 21 patients with unilateral FAI and 21 controls. Latencies were collected during a random inversion perturbation while walking. EMD measures were collected during stance using a percutaneous stimulus. Two-way ANOVAs were used to detect differences between leg (affected, unaffected) and group (FAI, Control). Functionally unstable ankles displayed delayed peroneus longus (PL) latencies and EMD when compared to the unaffected leg and a matched control group. Peroneal latency and EMD deficits could contribute to recurrence of ankle injury in FAI subjects. How these deficits are associated with the chronic symptoms associated with FAI remains unclear, but gamma activation and subsequent muscle spindle sensitivity likely play a role.