Japanese encephalitis (JE) is one of the most frequent causes of viral encephalitis in humans and belongs to the family of flavi viruses (Flaviviridae). Japanese Encephalitis Virus (JEV) is transmitted by mosquitoes and vectors from other organisms, so it is also known as a mosquito-borne disease of the Japanese encephalitis virus, which includes both positive-sense ssRNA (single stranded RNA). Includes 11 kb and several structural proteins (C, M and E) and 2 non-resistant proteins that are Non-Structural (NS) (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) of these, E protein plays an important part in immunogenicity, virus-cell membrane fusion, infection, and virus maturation. The capsid protein C plays a critical role in virus budding by attaching to the cell membrane and functions in the Nucleocapsid in the assembly of viral RNA. In this study, we have identified potential inhibi tors of JEV protein. Three proteins viz. Uniprot IDs P0DOH9, P0DOK8 and G3FEX6 were selected, with POLS_JAEV5 struc tural polyprotein, POLS_JAEVM structural polyprotein and POLG_JAEVM (genome polyprotein Japanese encephalitis virus (strain M28) (JEV)) respectively. 6 ligand i.e. Prechlorperazine, Chlorpromazine Hydrochloride, Chlorpromazine Methoiodide, Methochlorpromazine, Chloracyzine and N-Dimethylmethanimidamide were selected to perform the docked again protein based on literature studies. Docking was carried out using the Schrodinger application software using Glide Dock methods. The dock ing result of all three proteins against ligand suggests that Chlorpromazine Hydrochloride is the best inhibitor indicating a docking score of range from is -4.954. This study identified a potential ligand against JEV and can be further used for drug discovery and development.