This time-stratified case-crossover study aimed to quantify the impact of floods on daily Japanese encephalitis(JE)cases from 2007 to 2012 in Nanchong city of Sichuan Province,China.Using conditional logistic regression analysis,we calculated the odds ratios(ORs)and 95%confidence intervals(Cls)at different lagged days,adjusting for daily average temperature(AT)and daily average relative humidity(ARH).A total of 370 JE cases were noti-fied during the study period,with the median patient age being 4.2 years.The seasonal pattern of JE cases clus-tered in July and August during the study period.Floods were significantly associated with an increased number ofJE cases from lag 23 to lag 24,with the strongest lag effect at lag 23(OR = 2.00.95%Cl:1.14-3.52).Similarly,AT and ARH were positively associated with daily JE cases from lag 0 to lag 8 and from lag 0 to lag 9.respectively.Floods,with AT and ARH,can be used to forecast JE outbreaks in the study area.Based on the results of this study,recommendations include undertaking control measures before the number of cases increases,especially for regions with similar geographic,climatic,and socio-economic conditions as those in the study area.