IntroductionBalance impairments frequently occur after stroke. Achieving effective core trunk stability is the key to improving balance ability. However, there is still a lack of advanced well-defined rehabilitation protocols for balance improvement in patients with stroke. Intermittent theta-burst stimulation (iTBS) is a non-invasive brain activity modulation strategy that can produce long-term potentiation. The cerebellar vermis is a fundamental structure involved in balance and motor control. However, no study has demonstrated the therapeutic effect and potential mechanism of cerebellar vermis iTBS on balance after stroke.Methods and analysisThis study will be a prospective single-centre double-blind randomised controlled clinical trial with a 3-week intervention and 3-week follow-up. Eligible participants will be randomly allocated to the experimental group or the control group in a 1:1 ratio. After routine conventional physical therapy, patients in the experimental group will receive cerebellar vermis iTBS, whereas patients in the control group will receive sham stimulation. The overall intervention period will be 5 days a week for 3 consecutive weeks. The outcomes will be measured at baseline (T0), 3 weeks postintervention (T1) and at the 3-week follow-up (T2). The primary outcomes are Berg Balance Scale and Trunk Impairment Scale scores. The secondary outcomes are balance test scores via the Balance Master system, muscle activation of the trunk and lower limbs via the surface electromyography recordings, cerebral cortex oxygen concentrations measured via the resting-state functional near-infrared spectroscopy, Fugl-Meyer Assessment of Lower Extremity and Barthel index scores.Ethics and disseminationThis study was approved by the West China Hospital Clinical Trials and Biomedical Ethics Committee of Sichuan University. All participants will sign the informed consent form voluntarily. The results of this study will be published in peer-reviewed journals and disseminated at academic conferences.Trial registration numberChiCTR2200065369.