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Abstract Background Repetitive transcranial magnetic stimulation (rTMS) has been reported to treat muscle spasticity in post-stroke patients. The purpose of this study was to explore whether combined low-frequency rTMS (LF-rTMS) and cerebellar continuous theta burst stimulation (cTBS) could provide better relief than different modalities alone for muscle spasticity and limb dyskinesia in stroke patients. Methods This study recruited ninety stroke patients with hemiplegia, who were divided into LF-rTMS+cTBS group (n=30), LF-rTMS group (n=30) and cTBS group (three pulse bursts at 50 Hz, n=30). The LF-rTMS group received 1 Hz rTMS stimulation of the motor cortical (M1) region on the unaffected side of the brain, the cTBS group received cTBS stimulation to the cerebellar region, and the LF-rTMS+cTBS group received 2 stimuli as described above. Each group received 4 weeks of stimulation followed by rehabilitation. Muscle spasticity, motor function of limb and activity of daily living (ADL) were evaluated by modified Ashworth Scale (MAS), Fugl-Meyer Assessment (FMA) and Modified Barthel Index (MBI) scores, respectively. Results The MAS score was markedly decreased, FMA and MBI scores were markedly increased in the three groups after therapy than before therapy. In addition, after therapy, LF-rTMS+cTBS group showed lower MAS score, higher FMA and MBI scores than the LF-rTMS group and cTBS group. Conclusion Muscle spasticity and limb dyskinesia of the three groups are all significantly improved after therapy. Combined LF-rTMS and cTBS treatment is more effective in improving muscle spasticity and limb dyskinesia of patients after stroke than LF-rTMS and cTBS treatment alone.