Objective: To compare the effects of Wii and conventional training on functional abilities and neurocognitive function in basketball-players with Functional Ankle Instability (FAI). Design: Single-blind matched randomized clinical trial study. Setting: Outpatients setting. Participants: Fifty-four basketball-players were randomly assigned to the Wii and control group. Interventions: All athletes in the Wii group ( n = 27) performed Wii Fit Plus games; and in the control group ( n = 27), they performed conventional training three days a week for 12 sessions. Main outcome measures: To assess functional performance and neurocognitive function, we used hop tests (8-hop, side hop, and single hop) and Deary-Liewald Reaction Time Task (DLRT), respectively. DLRT measured simple and choice reaction time and error rate. Measures were taken at baseline, four weeks, and eight weeks after baseline. Results: In all 54 athletes completed the study. The results showed no significant differences for all hop tests in between-group comparison but the neurocognitive function showed significant improvements in the Wii group compared to the control group ( P < 0.05). Mean (SD) for 8-hop and side hop tests for the involved limb, and simple and choice reaction time four weeks after baseline in the control group were 10.15 (1.02), 12.36 (1.31), and 339.10 (41.57), 530.52 (53.36), respectively and in the Wii group, were 10.46 (1.23), 12.40 (1.31), and 295.25 (13.16), 431.19 (33.46), respectively. Conclusion: Based on our results, both training protocols were equal to positively affect functional abilities. Besides, Wii training improved neurocognitive function and can be applied in FAI rehabilitation protocols.