(1R,2S)-Ethyl 1-amino-2-vinylcyclopropanecarboxylate (VCPA), is a key intermediate for anti-hepatitis C virus drugs. In this study, we developed an efficient manufacturing method of intermediate for (1R,2S)-VCPA by enzymatic desymmetrization of a malonate diester derivative. In synthesis scheme of VCPA (1S,2S)-1-(ethoxycarbonyl)-2-vinylcyclopropanecarboxylic acid (VCPME) is the monoester intermediate, which is converted from 2-vinylcyclopropane-1,1-dicarboxylate diethyl ester (VCPDE). As a result of esterase screening for producing (1S,2S)-VCPME from VCPDE by enzymatic desymmetrization, p-nitrobenzyl esterase from Bacillus subtilis NBRC3027 (PNBE3027) showed high enantioselectivity (more than 90% e.e.). Based on the homology model of PNBE3027, a library of mutants with the substitution of L70, L270, L273, and L313 in substrate-binding pocket was created for improvement in enantioselectivity. (1S,2S)-VCPME produced by the best variant harboring L70D, L270Q, L273R, and L313M showed 98.9% e.e. of enanthiopurity. Furthermore, preparative scale production of (1S,2S)-VCPME using the quadruple mutant was achieved. Our investigations present a new efficient process for (1R,2S)-VCPA using esterase and diverse to be applied for the industrial scale production.