An enzymatically enantioselective transesterification procedure for the synthesis of (S)-suprofen ester prodrugs from racemic 2,2,2-trifluoroethyl suprofen ester was developed by using Candida rugosa lipase as the best biocatalyst in cyclohexane. From the performance of lipase enantioselectivity and activity, 3-diethylamino-1-propanol, 2-N-morpholinoethanol and diethylene glycol were selected as the best acyl accepters among the screened alcohol containing an N,N-dialkylamino or ethylene glycol moiety. Alcohol concentration and water content was found to have profound effects on the enzyme activity and the yields of (S)-ester product and (S)-suprofen byproduct. An enhancement of the productivity for the desired (S)-ester product was obtained by comparing the result with that in an enantioselective esterification process.