Abstract: Objective To analyze the epidemiological characteristics of Japanese encephalitis (JE) in Chongqing from 2006 to 2015, and to provide targeted and scientific preventive measures for the control of JE epidemic. Methods Descriptive epidemiology was used in this study. The statistical analysis system (SAS) software was employed to perform statistical analysis. Results A total of 1,611 JE cases were reported in Chongqing from 2006 to 2015. The incidence rate reduced from 0.72/100,000 in 2006 to 0.12/100,000 in 2015, with an annual drop of 17.67% and an annual average incidence rate of 0.49/100,000. 31 cases were dead. The average annual mortality rate was 0.009/100,000, and the average annual fatality rate was 1.62%. The incidence rate of males (0.57/100,000) was significantly higher than that of females (0.40/100,000) (P<0.05). All of the 39 counties had reported cases. The incidence was sporadic, mainly in Dazu District (129 cases, 8.00%), Fengdu County (123 cases, 7.64%), Kaixian County (114 cases, 7.08%) and Dianjiang County (97 cases, 6.02%). The incidence was obviously seasonal, the morbidity and mortality mainly concentrated in July and August (1,530 cases, 94.97%). The age of onset was 1-7 years old, accounting for 73.43%. The age of death was mainly 1-3 years old, with the median age of 2 years old. As for occupation distribution of the cases, scattered children accounted for 55.62%. In all cases, there were 698 cases (43.33%) of clinical diagnosis, and 913 cases (56.67%) of laboratory confirmed diagnosis. The main symptoms were fever (89.63%) and sleepiness (72.32%). The cases with vaccine vaccination history accounted for 18.37%, and those without accounted for 26.88%. And the immune history of 54.75% of the cases was unknown. Conclusions The incidence of JE in Chongqing City decreased year by year from 2006 to 2015. The surveillance in epidemic seasons should be strengthened in the future. On the basis of continuous routine immunization, the immunization should focus on children aged 1-5 years in areas with relatively high incidence, and at the same time the quality of case investigation and laboratory diagnosis should be improved.