Background: Stroke often results in significant motor impairments, particularly in the upper limbs, which can severely impact functional independence and quality of life. Conventional rehabilitation methods provide limited recovery, necessitating the exploration of adjunctive therapies to enhance motor function. Intermittent theta burst stimulation (iTBS) is a brain stimulation technique that has shown promise in improving motor function after stroke. This study was conducted to investigate whether iTBS targeting ipsilesional primary motor cortex can induce improvements of the paretic upper limb and physiological changes in cortical excitability in subacute stroke patients.Methods: 50 patients were randomized assigned to either iTBS or sham stimulation across 10 sessions. Motor function, symptom severity, muscle tone, and functional independence were evaluated. Additional measures included rest motor threshold (RMT), oxygenated hemoglobin concentration.Results: Both the iTBS and sham groups showed significant improvements in National Institutes of Health Stroke Scale (NIHSS) (iTBS: p = 0.002; sham: p = 0.039), Fugl-Meyer Assessment (FMA) (iTBS: p < 0.001; sham: p = 0.005), and Modified Barthel Index (MBI) (iTBS: p < 0.001; sham: p = 0.002) scores post-intervention. Only the iTBS group demonstrated significant improvements in Modified Ashworth Scale (MAS) (p < 0.001), Wolf Motor Function Test (WMFT) (p < 0.001), and RMT (p = 0.016). The iTBS group exhibited a trend toward greater improvements in MAS (p = 0.001), WMFT (p = 0.002), and MBI (p < 0.001). RMT in contralateral Primary motor cortex (M1) was significantly lower in the iTBS group (p = 0.016), and functional connectivity between each M1 regions was notably enhanced (p = 0.049).Conclusion: These findings suggest that iTBS may offer additional benefits in improving functional task performance and cortical connectivity in subacute stroke patients.Clinical trial registration: https://www.chictr.org.cn/showproj.html?proj=193454, Identifier ChiCTR2300072415.

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