Flaviviruses are the causative agents of viral hemorrhagic fever (VHF) globally and have demonstrated the capacity to result in fatal outcomes if not managed effectively. Among different types of flaviviruses, dengue (DENV) and Japanese encephalitis (JEV) viruses are the most common in tropical and subtropical countries. While vaccines have been developed and licensed for both DENV and JEV, effective treatment options remain sparse. Hence, there is a pressing need to develop small molecules that can target machineries crucial for virus replication and remain conserved across different flaviviruses, thereby could serve as a promising therapeutic option. This study outlines the synthesis of novel thiazole compounds as flavivirus NS2B-NS3 protease inhibitor and characterization of their antiviral activity against DENV and JEV. We synthesized a heterocyclic template derived from a substrate-based retrotripeptide dengue protease inhibitor, leading to 48 thiazole derivatives. Two compounds, 3aq and 3au demonstrated significant inhibition of dengue virus protease activity