Objective: To report the neurologic prognosis and autoimmune complications of 16 cases of childhood herpes simplex virus encephalitis. Methods: The study was conducted at Şanliurfa Training and Research Hospital, Turkey from June 2017 to August 2019. The study included 16 pediatric patients aged between 6 months and 17 years (median age 77.7 months) who were diagnosed with herpes simplex virus type 1 encephalitis by pediatric infectious disease and pediatric neurology clinics. Patients were followed using patient records, and interviews at the pediatric neurology clinic or via the telephone. Clinical and demographic data, received therapies, neurologic prognosis and complications were evaluated. Results: Patients with and without autoimmune encephalitis were compared in terms of age, sex, symptom duration before treatment, initial cerebrospinal fluid protein, glucose, red blood count and white blood count but no significant difference was found. Autoimmune complications were seen in four patients. N-methyl-D-Aspartate encephalitis was observed in three patients and choreoathetosis was seen in one patient. The average follow-up period was 48.3 months. Twenty-five percent of the patients were receiving multiple antiepileptic drug (AED) treatment, 43.8% were receiving single AED treatment and 31.3% were not receiving AED treatment at the end of the follow-up. Motor disability was observed in 12.5% and drug-resistant epilepsy was observed in 6.3% who had autoimmune complications. Conclusions: Seizures and movement disorders were controlled with immunotherapy and autoantibodies should be studied routinely. Treatment should be started early upon recognition of autoimmune complications through follow-up by measuring autoantibody levels and clinical examination results. Effective prevention and curative treatment modalities are needed to avoid herpes simplex virus encephalitis complications.