Background: Acute encephalitis syndrome (AES) is a public health problem in India. One of the causes is the Japanese encephalitis (JE), but in many patients this infection can be ruled out. The current hospital-based surveillance was conducted on patients with AES and JE. No comparative study on the long-term outcomes of JE vs. non-JE AES was available from India and there was no study on socioeconomic impact of the illness. Objectives: The current study aimed at comparing the long-term outcomes of JE vs. non-JE AES and studying the socioeconomic impact of AES on the population of Uttar Pradesh, India. Methods: Patients with AES discharged from hospital were followed-up by hospital or home visits, or telephone interviews. Functional outcomes and sequelae were compared between the patients with JE and non-JE AES by the Glasgow outcome scale (GOS), Liverpool outcome scale (LOS), and child & adolescent scale of participation (CASP). Socioeconomic impact and coping mechanisms were studied by the semi-structured qualitative methods. Results: A total of 91 patients (29 with JE, 62 with non-JE AES) were followed-up based on the mean (SD) duration of 21.9 (5.6) months after discharge from hospital. Functional outcomes were significantly worse in the cases with JE, but there was no significant difference in CASP scores between the groups. Only 4 patients with JE got financial help from the government. In the rest, almost all the expenses for travel, hospitalization, drugs, and investigation were borne by the families themselves. Most of the families borrowed money from relatives, while some mortgaged or sold their land and/or jewelry. Rehabilitation services were seldom available as it needed travelling to cities. The joint family system has a cushioning effect, however, providing physical and mental support. Conclusions: AES is a serious illness with severe long-term sequelae in survivors. Functional outcomes got worse in the patients with JE compared with the ones with non-JE AES. The illness had a severe socioeconomic impact and all expenses should be borne by poor families. Rehabilitation remained an unmet need. Some supports were provided through the joint family system.