Objective To investigate the clinical characteristics of autoimmune encephalitis (AE) in children with meningeal thickening and enhancement. Methods The clinical data of children diagnosed with AE and their brain magnetic resonance imaging (MRI) showing meningeal thickening with enhancement from December 2019 to February 2022 were retrospectively collected and analyzed, and the prognosis was followed up. Results A total of two boys were enrolled with onset age of 5 and 12 years old, respectively. The initial symptom of both patients was status epilepticus and disturbance of consciousness. Of them, case 1 had preceding infection, and still experienced repeated seizures during hospitalization, accompanied by gradual speech dysfunction and psycho-behavioral abnormality. The cerebrospinal fluid (CSF) results of case 1 indicated slightly leukocytosis, elevated protein (691.5mg/L) and significantly increased immunoglobulins (IgG 68.9mg/L, IgA 5.32mg/L and IgM 3.72mg/L). The antibodies associated with AE was negative in either serum or CSF. Case 2 was accompanied by central respiratory failure. The CSF results indicated slightly leukocytosis, elevated protein (617.6 mg/L) and IgA (3.17 mg/L), and positive anti-AMPAR1 antibody in serum. The serum and CSF next generation sequencing of pathogen was negative in both patients. Brain MRI of both patients showed meningeal thickening and enhancement. The electroencephalogram of the two patients showed background slow wave, and case 1 was accompanied by epileptic discharge. Two cases were diagnosed with AE. Simultaneously, the MRI findings of both was consistent with the feature of hypertrophic pachymeningitis (HP). Both of them obtained good prognosis after immunotherapy and anti-epileptic drug treatment. Conclusions For the children with meningeal thickening and enhancement on head MRI, the detection of AE-related antibodies can be completed in time. Early diagnosis and timely treatment are of great significance for improving prognosis.