The purpose of this study was to investigate the effects of isokinetic exercise on strength, joint position sense and functionality in recreational athletes with functional ankle instability (FAI). Strength, proprioception and balance of 24 recreational athletes with unilateral FAI were evaluated by using isokinetic muscle strength measurement, ankle joint position sense and one leg standing test. The functional ability was evaluated using five different tests. These were; single limb hopping course (SLHC), one legged and triple legged hop for distance (OLHD-TLHD), and six and cross six meter hop for time (SMHT-CSMHT). Isokinetic peak torque of the ankle invertor and evertor muscles were assessed eccentrically and concentrically at test speeds of 120 degrees /s. Isokinetic exercise protocol was carried out at an angular velocity of 120 degrees /s. The exercise session was repeated three times a week and lasted after 6 weeks. At baseline, concentric invertor strength was found to be significantly lower in the functionally unstable ankles compared to the opposite healthy ankles (p < 0.001). This difference was not present after executing the 6 weeks exercise sessions (p > 0.05). Ankle joint position sense in the injured ankles declined significantly from 2.35 +/- 1.16 to 1.33 +/- 0.62 degrees for 10 degrees of inversion angle (p < 0.001) and from 3.10 +/- 2.16 to 2.19 +/- 0.98 degrees for 20 degrees of inversion angle (p < 0.05) following the isokinetic exercise. One leg standing test score decreased significantly from 15.17 +/- 8.50 to 11.79 +/- 7.81 in the injured ankles (p < 0.001). Following the isokinetic exercise protocol, all of the worsened functional test scores in the injured ankles as compared to the opposite healthy ankles displayed a significant improvement (p < 0.01 for OLHD and CSMHT, p < 0.001 for SLHC, TLHD, and SMHT). These results substantiate the deficits of strength, proprioception, balance and functionality in recreational athletes with FAI. The isokinetic exercise program used in this study had a positive effect on these parameters.