We aimed to estimate the coverage of Japanese encephalitis (JE) vaccination in central India to help explain the continued occurrence of JE disease despite routine vaccination. We implemented a 30-cluster survey for estimating the coverage of JE vaccination in the medium-endemic areas implemented with JE vaccination in central India. The parents were enquired about the uptake of the JE vaccine by their children aged 2 to 6 years, followed by verification of the immunization cards at home along with reasons for non-vaccination. Vaccination coverage was reported as a percentage with 95% confidence intervals. We estimated high coverage of live-attenuated SA 14-14-2 JE vaccination in Maharashtra (94.8%, 95% CI 92.7-96.3) and Telangana (92.8%, 90.0-94.9). The vaccination card retention was 90.3% in Maharashtra and 70.4% in Telangana state. There were no gender differences in coverage in both states. A similar level of JE vaccination coverage was observed during the year 2013 to 2021 in both states. In Maharashtra, the maximum age-wise coverage was 96.6% in the >60 months age category, whereas in Telangana it was in the <24 months age category (97.2%). The timeliness of JE vaccination was appropriate and similar in both states. We found very good agreement between JE and Measles-Rubella vaccinations administered simultaneously. The reasons for non-vaccination were the shortage of vaccines and the parental migration for work. The coverage of Japanese encephalitis vaccination was high in medium-endemic regions in central India. Vaccination effectiveness studies may help further explain the continued incidence of Japanese encephalitis. This article is protected by copyright. All rights reserved.