Forty adults with unilateral functional ankle instability (FAI) were randomized to receive isokinetic eccentric training (n = 20) or isokinetic concentric training (n = 20) targeting ankle dorsiflexor and evertor muscles using a Biodex dynamometer, three times per week for twelve weeks. The primary outcome of interest was postural control of the affected limb (static sway area and length; dynamic total offset index) assessed on the Pro-Kin 254P platform. Secondary outcomes included ankle dorsiflexion and eversion relative peak torque (RPT) and dorsiflexion/plantarflexion (D/P) and eversion/inversion (E/I) torque ratios at 60°/s and 180°/s. Outcomes were assessed at baseline and after 12 weeks. Overall, the results of the study revealed that eccentric training produced larger improvements in dynamic postural control (notably a 23.8% reduction in total offset index), static sway area, dorsiflexion and eversion strength, and D/P and E/I torque ratios than concentric training, whereas sway length did not differ significantly between groups. These findings suggest that incorporating high-intensity isokinetic eccentric work into rehabilitation may better restore neuromuscular control and strength balance in FAI than concentric-only protocols.