Background <p>Despite diagnostic advancements, high rates of unidentified acute encephalitis cases persist among pediatric patients, and novel causative agents are emerging. This study investigates features of pediatric acute encephalitis cases, evaluates the impact of diagnostic improvements and identifies risk factors for sequelae.</p> Methods <p>We analysed acute encephalitis cases (aged 0 to 18 years) from January 2006 to December 2023. We compared epidemiological, clinical, laboratory, electroencephalographic, and neuroimaging features between patients with known and unknown, as well as infective and non-infective etiology, and assessed factors associated with sequelae.</p> Results <p>Among 235 acute encephalitis cases (50.2% males, median age 96 months), etiology was identified in 62.1%, with acute disseminated encephalomyelitis being the most common (44.2%). Infectious agents were confirmed in 28.9% cases. Patients with known etiology had longer hospital stay (<i>p</i> = 0.041), higher rates of abnormal MRI findings (<i>p</i> = 0.001) and sequelae at discharge (<i>p</i> = 0.005). Younger age (aOR = 0.80, <i>p</i> = 0.015), abnormal MRI findings (aOR = 2.98, <i>p</i> = 0.009), non-infectious etiology (OR = 2.88, <i>p</i> = 0.006) and higher CSF protein levels (aOR = 5.39, <i>p</i> = 0.017) were associated with sequelae. Etiology detection rate did not differ significantly after the introduction of autoimmune encephalitis panel and meningitis-encephalitis panel (66.2% vs. 60.9% vs. 62.5%, <i>p</i> = 0.768).</p> Conclusion <p>Immune-mediated causes of acute encephalitis are increasing. Despite diagnostic improvements, the rates of successful etiology determination are still suboptimal. Neuroradiologic assessment should be prioritized, as it enhances the identification of the underlying cause and can serve as a prognostic factor in determining outcomes.</p>