This invention provides a method for screening compounds against Flavivirus. More specifically, this invention provides a method for screening compounds against Flaviviruses by using a persistent virus-infected cell system, including (a) establishment of persistent virus-infected cell lines, (b) preparation of monoclonal antibody by using said persistent virus-infected cell lines, (c) incubation of tested compounds with said persistent virus-infected cell lines, (d) determination of the inhibition effect of tested compounds or vaccines on Flavivirus by sandwich ELISA using said monoclonal antibody.