Unilateral neglect (UN) is a common complication after stroke, with limited effective treatment strategies. This study evaluates the therapeutic effects of intermittent theta-burst stimulation (iTBS) on the intact dorsolateral prefrontal cortex (DLPFC) in UN patients and explores the neurophysiological mechanisms.Twenty UN patients were randomly assigned to an iTBS or sham stimulation group, receiving 10 consecutive days of treatment. Clinical assessments and TMS-EEG recordings were performed before and after treatment.Patients receiving iTBS showed significant improvements in the Line Cancellation Test (p = 0.012). In addition, iTBS led to notable changes in cortical excitability and neural signal propagation. Specifically, the iTBS group exhibited a significant increase in the N100 component (p < 0.001). Time-frequency analysis also revealed a reduction in theta-band power in the affected frontal cortex post-treatment. At the network level, functional connectivity in the iTBS group was significantly enhanced, particularly within interhemispheric frontal and frontoparietal networks during the later stages of the treatment.iTBS effectively alleviates UN symptoms by modulating cortical excitability and enhancing functional connectivity, suggesting it as a promising therapeutic intervention for UN.© 2025 The Authors.