Background Japanese encephalitis virus (JEV) is a major threat to human health. Bangladesh is considering introducing a JEV vaccine, however, the investment case is hampered by a poor understanding of key aspects of JEV ecology, including underlying patterns of infection, the infection fatality ratio, and which host and vectors maintain transmission. Methods We conducted a seroprevalence study in individuals of all ages in Chapai Nawabganj, Bangladesh. We tested blood samples for anti-JEV antibodies using a novel assay that limits cross-reactivity with dengue virus, trapped mosquitoes, and collected information about potential host species. We combined our results with data from a pig census, human case data and healthcare seeking patterns, all from the same region, and used mathematical models to recover risk factors for infection, and underlying probabilities of severe disease and death. Findings We found 14.3% (203/1455) of participants had antibodies against JEV. We estimated 0.5% of the susceptible population gets infected each year, however, infection risk was spatially heterogeneous, with the presence of pigs in the vicinity being the most important predictor of seropositivity. We identified 10 different known mosquito vectors for JEV. We estimated that 1 in 1,000 infections result in severe disease, 1 in 10,000 result in death, and 76% of severe cases are missed by surveillance systems. Interpretation JEV infection risk is highly spatially heterogeneous, with the underlying potential of vaccines linked to the distribution of pig-raising communities.