Objective: To explore the clinical application effect of acupuncture combined with repetitive transcranial magnetic stimulation (rTMS) in the treatment of children with persistent vegetative state (PVS). Method: 112 children with PVS who were treated in the Pediatric rehabilitation department of our hospital from January 2022 to December 2023 were selected as the research subjects. The children were divided into the control group (n=56) and the observation group (n=56) according to the random number table method. The control group received conventional comprehensive rehabilitation treatment. The observation group received acupuncture combined with rTMS treatment on the basis of the control group. The recovery of consciousness [Pediatric Coma Recovery Scale (PCRS)], the recovery of consciousness state and function [Glasgow Coma Scale (GCS) score, Pediatric Coma Recovery Scale (PCRS) score], the improvement rate of electroencephalogram (EEG) activity and the incidence of adverse reactions were analyzed and compared between the two groups. Result: The consciousness recovery rate of the observation group was significantly higher than that of the control group (P<0.05). After treatment, the GCS and PCRS scores of both groups were significantly improved compared with those before treatment, and the GCS and PCRS scores of the observation group after treatment were significantly higher than those of the control group (P<0.05). The improvement rate of electroencephalogram activity in the observation group was significantly higher than that in the control group (P<0.05). There was no significant difference in the incidence of adverse reactions between the two groups (P>0.05). Conclusion: Acupuncture combined with rTMS in the treatment of children with PVS can increase the rate of consciousness recovery in children, improve electroencephalogram activity, and has good safety.