BackgroundWe estimated the incidence of Japanese encephalitis (JE) and acute encephalitis syndrome (AES) following routine immunization with the live-attenuated SA 14-14-2 JE vaccine.MethodsWe implemented enhanced surveillance of AES and JE hospitalizations in endemic districts in Maharashtra and Telangana States during 2015–2016 and 2018–2020. We estimated incidence and compared differences in the incidence of JE and AES between two states, and vaccinated and unvaccinated districts during two study periods. We also considered secondary data from public health services to understand long-term trends from 2007 to 2020.ResultsThe annual AES incidence rate of 2.25 cases per 100,000 children in Maharashtra during 2018–2020 was significantly lower than 3.36 cases per 100,000 children during 2015–2016. The six JE-vaccinated districts in Maharashtra had significantly lower incidence rates during 2018–2020 (2.03, 95% CI 1.73–2.37) than in 2015–16 (3.26, 2.86–3.70). In addition, the incidence of both JE and AES in two unvaccinated districts was higher than in the vaccinated districts in Maharashtra. Telangana had a lower incidence of both JE and AES than Maharashtra. The AES incidence rate of 0.95 (0.77–1.17) during 2018–2020 in Telangana was significantly lower than 1.67 (1.41–1.97) during 2015–2016.ConclusionsThe annual incidence rate of Japanese encephalitis was < 1 case per 100,000 children. It indicated accelerated control of Japanese encephalitis after routine immunization. However, the annual incidence of acute encephalitis syndrome was still > 1 case per 100,000 children. It highlights the need for improving surveillance and evaluating the impacts of vaccination.