Immune-mediated or autoimmune encephalitis (AE) is a relatively new, rare and elusive form of encephalitis in children. We retrospectively collected seropositive children (0–18 years old) with well characterized antibodies through 3 reference laboratories in Israel. Clinical symptoms, MRI and EEG findings and treatment courses were described. A total of 16 patients were included in the study, with 10 females. Anti NMDA encephalitis was most common followed by anti HU and anti mGLuR1. Psychiatric symptoms, abnormal movements, seizures and behavioral changes were the most common presentation. Pathological MRI and EEG findings were described in 37% and 56% of children, respectively. Treatment with corticosteroids, Intravenous immunoglobulins (IVIG) was first line in most children. Following inadequate response children were treated with plasmapheresis and/or rituximab. Two patients relapsed following both first and second line protocols. In terms of long term prognosis, 9 children (56%) had one or more residual behavioral, psychiatric or neurologic findings. Three children required hospitalization for rehabilitation. AE remains a rare diagnosis with variable presenting symptoms, requiring a high index of suspicion. Consensus recommended treatment is generally effective in the pediatric population. Female gender was associated with a higher chance of severe disease. Larger cohorts would be needed to identify prognostic factors in the pediatric population.