Objective Comorbid autonomic nervous system dysfunction affects the overall prognosis of children with Guillain-Barré syndrome (GBS), whereas systematic research on the course of autonomic nervous system dysfunction and the process of neurological function recovery in these children remains scarce. This study aims to investigate the clinical characteristics and neurological function recovery of GBS children complicated with autonomic nervous system dysfunction. Methods A retrospective analysis was conducted on the clinical data of children with GBS who visited Wuhan Children’s Hospital, Tongji Medical College from May 2017 to August 2023. The children were divided into two groups, with and without autonomic dysfunction, and a comparative analysis of key clinical indicators between the two groups were conducted. Results A total of 92 children with GBS were enrolled, including 58 boys (63.0%), with a median age of 5.0 (3.4-8.4) years. None of the children presented with autonomic nervous system dysfunction as the initial symptom. Autonomic nervous system dysfunction developed in 40 cases (43.5%) during the disease course, with the median time from disease onset to the occurrence of autonomic nervous system dysfunction being 9 (4-13) days. Cardiovascular complications were the most common autonomic symptoms, including 16 cases of tachycardia, 12 cases of arrhythmia, 5 cases of hypertension, 4 cases of atrioventricular block, 3 cases of orthostatic hypotension, and 2 cases of bradycardia. Other symptoms included 4 cases of diarrhea, 2 cases of constipation, 7 cases of urinary retention, and 3 cases of hyperhidrosis. Compared with GBS children without autonomic nervous system dysfunction, those with this complication had significantly higher proportions of assisted ventilation requirement and combined immunotherapy plus plasma exchange, longer hospital stays, and longer time to recovery of independent ambulation (P<0.05). Autonomic nervous system function recovered within 3 months in all children. At the 3-month follow-up, among all children with abnormal nerve conduction, only 39.0% (30/77) achieved recovery of nerve conduction velocity, while the recovery rate of clinical symptoms was 67.5% (52/77). Conclusions Autonomic nervous system dysfunction affects the treatment and prognosis of children with Guillain-Barré syndrome (GBS). However, autonomic nervous system dysfunction in these children achieves a favorable recovery, and its recovery time precedes that of nerve conduction impairment.