OBJECTIVE: To investigate the effects of a 12-week isokinetic eccentric training program on postural control and ankle muscle strength in individuals with functional ankle instability (FAI). METHODS: In this randomized controlled trial, 42 participants with unilateral FAI were randomly assigned to either an experimental group (n = 21), receiving isokinetic eccentric training, or a control group (n = 21), receiving isokinetic concentric training. Both groups trained three times per week for 12 weeks. One participant from each group dropped out during the intervention, resulting in 20 participants per group included in the final analysis. Primary outcomes included static and dynamic postural control assessed using the Pro-Kin 254P platform. Secondary outcomes were ankle dorsiflexion and eversion strength, as well as dorsiflexion/plantarflexion (D/P) and eversion/inversion (E/I) torque ratios measured with a Biodex System 4 Pro dynamometer at 60°/s and 180°/s. Between-group comparisons and effect sizes (Cohen's d) with 95% confidence intervals (CI) were reported. RESULTS: After 12 weeks, the experimental group demonstrated significantly greater improvements in postural control and ankle strength outcomes compared to the control group (p < 0.01). For dynamic postural control, the total offset index decreased by 23.8% in the eccentric group, showed a significant improvement with a very large effect size (Cohen's d = 2.06, 95% CI [1.29, 2.82], p < 0.001). Static postural control, measured by sway area, was reduced by 17.3% (Cohen's d = 0.81, 95% CI [0.16, 1.45], p = 0.015), while sway length did not reach statistical significance (Cohen's d = 0.55, 95% CI [-0.08, 1.18], p = 0.090). Regarding ankle strength, dorsiflexion relative peak torque (RPT) at 60°/s increased by 30.7% in the eccentric group (Cohen's d = - 0.79, 95% CI [-1.44, - 0.15], p = 0.016), while eversion RPT at 180°/s improved by 75.7% (Cohen's d = - 1.13, 95% CI [-1.79, - 0.46], p = 0.001). The D/P torque ratio at 180°/s exhibited a very large between-group difference (Cohen's d = - 2.18, 95% CI [-2.96, - 1.39], p < 0.001), and the E/I torque ratio at 60°/s demonstrated an extremely large effect size (Cohen's d = - 4.50, 95% CI [-5.67, - 3.34], p < 0.001). CONCLUSION: Isokinetic eccentric training significantly enhances postural stability and ankle muscle strength in patients with FAI. These improvements in torque symmetry and balance support the inclusion of eccentric training as an effective rehabilitation strategy to reduce reinjury risk and restore neuromuscular function.