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Abstract Background Chronic ankle instability (CAI) is a form of musculoskeletal disease that can occur after a lateral ankle sprain, and it is characterized by pain, recurrent ankle sprains, a feeling of “giving way” at the ankle joint, and sensorimotor deficits. There has been increasing evidence to suggest that plastic changes in the brain after the initial injury play an important role in CAI. As one modality to treat CAI, whole-body vibration (WBV) has been found to be beneficial for treating the sensorimotor deficits accompanying CAI, but whether these benefits are associated with brain plasticity remains unknown. Therefore, the current study aims to investigate the effect of WBV on sensorimotor deficits and determine its correlation with plastic changes in the brain. Methods The present study is a single-blind randomized controlled trial. A total of 80 participants with CAI recruited from the university and local communities will be divided into 4 groups: whole-body vibration and balance training (WBVBT), balance training (BT), whole-body vibration (WBV), and control group. Participants will be given the WBV intervention (25-38 Hz, 1.3-2 mm, 3-time per week, 6-week) supervised by a professional therapist. Primary outcome measures are sensorimotor function including strength, balance, proprioception and functional performance. Brain plasticity will be evaluated by corticomotor excitability, inhibition, and representation of muscles, as measured by transcranial magnetic stimulation. Activation of brain areas will be assessed through functional near-infrared spectroscopy. Secondary outcome measures are self-reported functional outcomes involving the Cumberland Ankle Instability Tool and the Foot and Ankle Ability Measure. All tests will be conducted before and after the WBV intervention, and at 2-week follow-up. Per‑protocol and intention-to-treat analysis will be applied if any participants withdraw. Discussion This is the first trial to investigate the role of brain plasticity in sensorimotor changes brought by WBV for individuals with CAI. As plastic changes in the brain have been an increasingly important aspect in CAI, the results of the current study can provide insight into the treatment of CAI from the perspective of brain plasticity. Trial registration Chinese Clinical Trial Registry (ChiCTR2300068972); registered on 02 March 2023.