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Introduction Hereditary spastic paraplegia (HSP) is a rare neurodegenerative disorder characterised by spasticity and weakness in both lower limbs due to axonal degeneration of the corticospinal tract. Motor dysfunction is a key clinical feature of HSP, severely impacting patients’ ability to work and perform daily activities. Intermittent theta burst stimulation (iTBS), a specific form of transcranial magnetic stimulation, can induce excitatory effects by modulating stimulation duration and interval. Recently, the central-peripheral-central closed-loop rehabilitation model has gained significant attention, and its core concept is to integrate central and peripheral interventions. The objective of this study is to evaluate the effect of central combined with peripheral iTBS on motor function in adults with HSP.Methods and analysis In this randomised controlled trial, 40 patients admitted to the First Affiliated Hospital of Fujian Medical University will be randomly assigned (1:1 ratio) to either active iTBS or sham iTBS groups. iTBS will be administered to the bilateral primary motor cortex and common peroneal nerve, delivering a total of 4800 pulses, five times a week for 2 weeks. Throughout the iTBS treatment period, participants will also engage in conventional rehabilitation training for 30 min, five times a week for 2 weeks. The primary outcome measure will be assessed using the 10 Metre Walk Test at baseline, postintervention and 4 weeks after the intervention ends. Secondary outcomes will include the Spastic Paraplegia Rating Scale, the Modified Ashworth Scale, the Medical Research Council scale, the Berg Balance Scale, Pro-Kin balance centre of pressure parameters, the Timed Up and Go Test, RealGait gait parameters and neuro-electrophysiological indicators. Additionally, any adverse events will be recorded.Ethics and dissemination This study was approved by the Ethics Committee of the First Affiliated Hospital of Fujian Medical University (Approval No.: MRCTA, ECFAH of FMU (2024)862). All participants will be required to provide written informed consent. The results of the study will be submitted for publication in peer-reviewed journals.Trial registration number ChiCTR2500097169.