Flavivirus causes arthropod-borne severe diseases that sometimes lead to the death. The Flavivirus species including Dengue virus, Zika virus and yellow fever virus are transmitted by the bite of Aedes mosquitoes. All these viral species target the people living in their respective endemic zone causing a high mortality rate. Recent studies show that immune factors present in the Ae. aegypti saliva is the hidden culprit promoting blood meal collection, suppressing host immune molecules and promoting disease establishment. This study was designed to develop a subunit vaccine using Aedes mosquito salivary proteins targeting the aforementioned Flaviviruses. Subunit vaccine was designed very precisely by combining the immunogenic B-cell epitope with CTL and HTL epitopes and also suitable adjuvant and linkers. Immunogenicity, allergenicity and physiochemical characterization were also performed for scientific validation. Molecular docking and molecular dynamics simulations studies were carried out to confirm the stable affinity between the vaccine protein (3D) and TLR3 receptor. At last, in silico cloning was executed to get the subunit vaccine restriction clone into pET28a vectro to express it in microbial expression system. Additionally, this study warrants the experimental evaluation for the validation purposes.