Introduction: The World Health Organization recommends mass vaccination campaigns in children under 15 years before introducing the Japanese Encephalitis (JE) vaccine into the routine immunization program as the most effective immunization strategy in JE disease-endemic countries. The study was conducted to assess the JE vaccine coverage during the recent mass vaccination campaign in five districts of Nepal in 2016.
 Methods: A stratified three-stage cluster design was used for this cross-sectional sample survey. The JE mass vaccination campaign of 2016 targeted children aged between 1-14 years, and the interview was conducted among systematically sampled households’ mothers and guardians of children aged between 2-15 years in 2017.
 Results: The coverage of the JE mass vaccination campaign in the year 2016 was 96.9%; the males had slightly higher coverage (97.4%) than females (96.6%). The vaccine utilization increased with an increase in age, 94.0%, 98.1%, and 99.1% coverage among children aged 2-5 years, 6-10 years, and 10-15 years, respectively. The school enrolled children were four-times (OR: 4.016, CI: 2.595–6.216) likely to be vaccinated than out-of-school children and association was statistically significant. Among 86 children who were not vaccinated, 45.3% were ill during the campaign. Besides, 6.6% of out of school children also didn’t get the vaccination. Only three in ten (30.4%) respondents knew that the JE vaccine was given to protect against JE disease or brain fever. More than one-third (36.3%) of respondents reported that the recommendation from the health workers was main reason for vaccinating their children. Only 1.1% of vaccinated children had minor issues following vaccination.
 Conclusion: Despite low awareness about the specific protection of the JE vaccine, the vaccination coverage was high during the JE mass vaccination campaign. Increasing awareness about the particular vaccine and including activities to vaccinate out-of-school children could help achieve universal coverage in future mass vaccination campaigns