Objective To retrospectively analyze the clinical features and prognosis of immune-related brainstem encephalitis in children. Methods The clinical data, treatment and prognostic follow-up results of children diagnosed with immune-related brainstem encephalitis in the Department of Neurology, from March 2017 to October 2022 were collected. Results A total of 13 children (8 boys and 5 girls) were included. The median age of first onset was 5.0 (1.9-7.1) years old, and 12 had precursor events within 1 month before onset. The common initial neurological symptoms in clinical manifestations were limb movement disorder (69.2 %, 9/13), facial paralysis (46.2 %, 6/13), and decreased consciousness level (46.2 %, 6/13). The common neurological signs during the course of the disease were cranial nerve involvement (76.9 %, 10/13), decreased muscle strength (69.2 %, 9/13) and decreased consciousness level (46.2 %, 6/13). In the acute stage, 30.8 % (4/13) of the children showed protein-cell separation in cerebrospinal fluid, 30.8 % (4/13) of the children had positive serum anti-GQ1b antibody, and 53.8 % (7/13) of the children had abnormal brain stem signals on head MRI. The immunotherapy during acute phase was intravenous methylprednisolone combined with immunoglobulin. Only 1 patient had poor effect, but improved after immunoadsorption therapy. The median follow-up time after discharge was 12 (6-24) months, during which there was no recurrence and only 2 cases of residual sequelae. Conclusions Immune-related brainstem encephalitis in children usually occurs at about 5 years of age with prodromal events. The common neurological symptoms and signs include limb paralysis, cranial nerve paralysis and decreased consciousness level. Most children with first-line immunotherapy have good outcomes and few neurological sequelae.