The invention relates to a chicken Flavivirus and an inactivated vaccine thereof and belongs to the field of veterinary epidemiology. The chicken Flavivirus is chicken Flavivirus strain FQ-C1 which is preserved in the China General Microbiological Culture Collection Center with preservation serial number: CGMCC No.4905. After the chicken Flavivirus strain FQ-C1 is inoculated to SPF (specified pathogen free) chick embryos, the allantoic fluids of the SPF chick embryos which die of transfection are collected, the allantoic fluids of the SPF chick embryos are inactivated with formaldehyde and then mixed with white oil which is used as an adjuvant, and the resulting mixture is emulsified to prepare an inactivated vaccine in the form of oil emulsion. The chicken Flavivirus inactivated vaccine provided by the invention does not cause any adverse effect on chickens and has high experimental safety. The vaccine can effectively control Flavivirus disease in chickens and helps reduce the losses and increase the breeding benefits of majority of chicken farmers in China.