Yellow fever virus (YFV) is a member of the Flavivirus genus within the Flaviviridae family. It is an enveloped single-stranded positive-sense RNA virus. Although the vaccine can effectively prevent YFV infection, the low coverage of vaccination and lack of effective antiviral drugs result in frequent outbreaks of YFV. YFV genome encoded proteins play important roles in basically all steps of viral infection. Therefore, the development of therapeutic drugs targeting YFV proteins is an effective measure to improve the therapeutic effect and reduce the mortality of this infectious disease. In this review, we briefly introduce the structure and function of the YFV genome encoded proteins, and summarize the research progresses and prospects of anti-YFV drugs targeting these proteins, so as to provide references for prevention and treatment of YFV infection.