Background: Myanmar is endemic for Japanese encephalitis (JE) and has experienced several outbreaks in recent years. The vector-borne disease control (VBDC) program has collected hospital-based surveillance data since 1974. There is an urgent need to collate, analyze, and interpret the most recent information. The study aimed to describe (i) hospital-based JE cases and deaths between 2012 and 2017, (ii) a catch-up vaccination campaign in children in 2017, and (iii) health service provider perceptions about JE in one township in 2018. Methods: This was a cross-sectional study of cases, deaths, and catch-up childhood vaccinations using secondary data from program records and a survey database of health service provider perceptions. Results: Between 2012 and 2017, there were 872 JE cases and 79 deaths with a case fatality rate of 91 per 1000; 2016 was the year with most cases and deaths. Most cases (n = 324) and deaths (n = 37) occurred in children aged 5-9 years. Large case numbers were reported in delta and lowland regions (n = 550) and during the wet season (n = 580). The highest case fatality rates were observed in the hills and coastal regions (120 and 112 per 1000, respectively). Nationwide coverage of the catch-up JE vaccination campaign among 13.7 million eligible children was 92%, with coverage lower in the hills and coastal regions (84%) compared with delta and lowland regions and plains (94%). More vaccinations (65%) occurred through school-based campaigns with the remainder (35%) vaccinated through community-based campaigns. Structured interviews in one township showed that service providers (n = 47) had good perceptions about various aspects of JE, although perceived benefits of specific vector control measures were poor: spraying/fumigation (38%), garbage removal (36%), larvicide use (36%), and drainage of standing/stagnant water (32%).