Aim: Long-Term Morbidity and Functional Outcome of Japanese Encephalitis in Children. Methods: A prospective study was conducted in the Department of Pediatrics, Shri Krishna Medical College and Hospital, Muzaffarpur, Bihar, India. Children aged up to 12 years admitted with acute encephalitis syndrome (AES) were subjected to laboratory tests for detection of JE. Anti-JE IgM antibody capture (MAC) ELISA was performed on cerebrospinal fluid and serum samples using ELISA kit. Diagnosis of JE was confirmed by detection of antiJE IgM antibody in cerebrospinal fluid (CSF), or both in CSF and serum samples. Patients with positive results were included in this study. Background demographic and relevant clinical data and results of various laboratory investigations including magnetic resonance imaging (MRI) of brain were noted. Discharged patients were followed up for two years at out-patient department and detailed clinical examination was done to document clinical status. Results: A total of 300 children with features of AES were screened, and 100 (33.33%) children (55% boys) were diagnosed with laboratory confirmed JE during the study period. Anti-JE IgM was detected in both CSF and serum in 80 children, and in only CSF in another 20 children. 20 cases (20%) died during the hospital stay. At the time of discharge, 30 children (30%) had severe sequelae, 9 (9%) had moderate sequelae, 10 (10%) developed minor sequelae, and 32 children (32%) showed full recovery as per LOS. Motor deficit was noted in 40 children (50%) at discharge; quadriparesis in 25, hemiparesis in 8, and monoparesis in 2 child. EEG was performed in 50 children, 35 (70%) were abnormal. Till the end of the study, 20 children (20%) were on AED. Among cases under follow-up, 60 children were schoolgoing. Poor scholastic performance was observed in 10 (20%) children in the long term; another 10 of them became drop-outs due to motor deficits, behavioral problems and apprehension of seizures. Conclusion: Considering high mortality and long term morbidities, preventive aspects of the disease need to be prioritized.