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Background The number of patients with prolonged disorders of consciousness (pDOC) is increasing. However, its clinical treatment remains challenging. To date, no studies have reported the effect of vagus nerve modulation (VNM) using repetitive transcranial magnetic stimulation (rTMS) in patients with pDOC. We aimed to evaluate the effect of vagus nerve magnetic modulation (VNMM) on pDOC patients. Methods We performed VNMM in 17 pDOC patients. The Revised Coma Recovery Scale (CRS-R), Glasgow scale (GCS), somatosensory evoked potentials (SEP) and brainstem auditory evoked potentials (BAEP) were assessed before and after treatment. Results Both CRS-R and GCS results showed significant improvement in p DOC patients after VNMM treatment. The CRS-R improved from 7.88 ± 2.93 to 11.53 ± 4.94. The GCS score also improved from 7.65 ± 1.9 to 9.18 ± 2.65. The number of BAEP grades I increased from 3 to 5 after treatment. The number of BAEP grades I increased from 3 to 5, grade II increased by 1, and grade III decreased from 4 to 1. Conclusion This study provides a preliminary indication of the potential of VNMM in the rehabilitation of pDOC patients. It provides the basis for a Phase 2 or Phase 3 study of VNMM in patients with pDOC.