Objective To explore the clinical features, treatments and prognosis of autoimmune encephalitis (AE) in children. Methods A total of 12 cases of children with AE who were admitted to Department of Neurology in Children′s Hospital, Capital Institute of Pediatrics from October 2014 to November 2016 were selected as research subjects. Among 12 cases of children with AE, there were 11 cases of children with anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis and 1 case of child with anti-leucine-rich glioma inactivated protein 1 (LGI1) antibody-associated encephalitis. Clinical cases data of 12 children with AE were retrospectively analyzed, which included clinical manifestations, auxiliary examinations, diagnosis, treatment and follow-up, to summarize the clinical characteristics, treatment and prognosis of AE in children. This study was in line with World Medical Association Declaration of Helsinki revised in 2013 and informed contents were obtained from the guardians of all patients. Results ①General clinical data: the average age of 12 children with AE was 7 years and 5 months, the average course of disease on admission was 20.5 d, and the ratio of male to female children was 5∶7. ②Clinical manifestations: most of patients were acute or subacute onset, the first symptoms could be abnormal emotions and behavior, fever along with headache, convulsion, speech disorder, fatigue and abnormal sensation, etc.. The main clinical manifestations of 11 children with anti-NMDAR encephalitis included psychiatric symptoms (90.9%, 10/11), sleep disorders (81.8%, 9/11), language, cognitive disorders or dyscinesia (72.7%, 8/11), seizures (54.5%, 6/11), disturbance of consciousness (45.5%, 5/11), dysautonomia (36.3%, 4/11). The main clinical manifestation of one child with anti-LGI1 antibody-associated encephalitis was sleep disorder. ③Results of laboratory examinations: routine examination results of cerebrospinal fluid were basically normal, and no tumors were found in 12 children by imaging screening. Among 12 children with AE, the cranial MRI examination of 6 children showed abnormal intracranial signals. Video-electroencephalogram examination of 8 children showed different degrees of slow waves background. Anti-NMDAR antibodies in cerebrospinal fluid of 11 children with anti-NMDAR encephalitis were positive or strongly positive, and anti-LGI1 antibody in cerebrospinal fluid of that child with anti-LGI1 antibody-associated encephalitis was positive. ④Results of treatment and followed-up: methylprednisolone and/or intravenous immunoglobulin (IVIG) were used for immunotherapy in 12 children with AE. The followed-up period was 12 to 27 months of 12 children, and among them, 9 cases were clinically cured, 2 cases had neurological sequelae of varying degrees, 1 case lost to follow-up just after discharge. ⑤Special manifestations: the clinical manifestation of case 1 was only visual impairment and case 12 was mainly sleep disorder. Three children under 6 years old were mainly characterized by recurrent convulsions, disturbance of consciousness or motor disturbance, and their conditions were serious, while the efficacy of the first-line immunotherapy was poor, so they all needed to carry out the second-line immunotherapy. Conclusions Anti-NMDAR encephalitis is the main type of AE in children, and anti-LGI1 antibody-associated encephalitis is also found in children. Neurological and psychiatric symptoms are the main clinical manifestations of children with AE but without specificity. Immunotherapy for AE is effective. Severe cases of AE should be combined with the second-line immunotherapy at early stage, and it is safer and more effective.