Flavivirus protease has been deemed a potential target for drug and therapeutics development due to its crucial role in viral replication. In this study we prepared a monoclonal antibody (mAb) against nonstructural protein 3 (NS3) protease portion of Japanese encephalitis virus (JEV), and evaluated its inhibitory effect for NS3 protease activity. First, a JEV NS3 protease-specific mAb (designated 2C2) was generated by the traditional cell fusion technique. Second, the binding specificity of 2C2 for NS3 protease was determined by indirect fluorescent assay and Western blotting. Finally, inhibitory effect of 2C2 for NS3 protease cleaving human stimulator of interferon gene was evaluated. Therefore, mAb 2C2 provides a potential diagnostic tool for differential diagnosis for patients who have been vaccinated with inactivated vaccine or naturally infected, and might be genetically reconstructed and optimized for new therapeutics development.