NS1 protein of Japanese encephalitis virus (JEV) is an important non-structural protein, which is able to induce protective immune response in target animals and can be used as specific serological diagnosis tool, but the epitopes on NS1 of JEV have not been identified. For epitope mapping, in this study, a series of 51 partially overlapping fragments covering entire NS1 protein were expressed with a GST-tag and then screened by a monoclonal antibody (mAb). Through enzyme-linked immunosorbent assay (ELISA), linear epitope-containing fragment, the overlapping region of NS1-18 and NS1-19 (residues 145-152), was located. Then a set of peptides derived from that overlapping region with deletions were expressed and subjected to ELISA and Western blot for further mapping purpose. Results indicated that the motif of (146)EHARW(150) is the minimal unit of the linear epitope recognized by that monoclonal antibody (mAb). Western blot showed that this epitope could be recognized by JEV-positive serum from pigs. Furthermore, it was found that the epitope is highly conserved among JEV strains through sequence alignments analysis. Notably, none of the homologous regions on NS1 proteins of other flavivirus could react with the mAb when they were tested for cross-reactivity, suggesting the potential clinical application of this epitope in differential diagnosis.