Filamentous phage display systems have been developed successfully to generate functional Fab antibody fragments. In this study, a recombinant Fab antibody fragment was successfully cloned from a murine monoclonal antibody 2H2 that can effectively neutralize Japanese encephalitis virus (JEV) in vitro. The recombinant Fab 2H2 antibody fragment expressed in Escherichia coli using the pComb3H phage vector resulted in a dose-dependent neutralization response using plaque reduction neutralization test. Molecular modeling of the Fab 2H2 indicated that the rational contact residues of the Fab 2H2 were targeted to the lateral surface of domain III of the JEV E protein. The combining sites of Fab 2H2 were mostly located at the variable region of the heavy chain genes. In vitro shuffling of the heavy-chain variable genes using pCom3H phage technology indicated that the sequence analysis of 10 high-affinity clones selected from the self-shuffling libraries presented no change in their amino acid sequences in 6CDRs, suggesting that the Fab 2H2 had evolved to be highly matured in the combining sites to the lateral surface of domain III. The information gained from this study may benefit the design of vaccines and therapeutic antibodies against JEV infection.