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Although previous studies have reported that meteorological factors might affect the risk of Japanese encephalitis (JE), the relationship between meteorological factors and JE remains unclear. This study aimed to evaluate the relationship between meteorological factors and JE and identify the threshold temperature. Daily meteorological data and JE surveillance data in Dazhou, Sichuan, were collected for the study period from 2005 to 2012 (restricting to May-October because of the seasonal distribution of JE). A distributed lag nonlinear model was used to analyze the lagged and cumulative effect of daily average temperature and daily rainfall on JE transmission. A total of 622 JE cases were reported over the study period. We found JE was positively associated with daily average temperature and daily rainfall with a 25-day lag and 30-day lag, respectively. The threshold value of the daily average temperature is 20°C. Each 5°C increase over the threshold would lead to a 13% (95% CI: 1-17.3%) increase in JE. Using 0 mm as the reference, a daily rainfall of 100 mm would lead to a 132% (95% CI: 73-311%) increase in the risk of JE. Japanese encephalitis is climate-sensitive; meteorological factors should be taken into account for the future prevention and control measure making, especially in a warm and rainy weather condition.