An analytical solution for the dynamic kinetic resolution of enzyme-catalyzed irreversible acyl transfer was employed to study the side-reaction effects on the yield and optical purity of the desired enantiomeric product. A lipase-catalyzed enantioselective thiotransesterification between (R,S)-naproxen 2,2,2-trifluoroethyl thioester and 4-morpho-line ethanol with in situ racemization of (R)-thioester using trioctylamine as the racemization catalyst in isooctane was designed as a model system to compare the theoretical predictions. Under an initial water activity of 0.113, adding trioctylamine was found to have profound effects on the hydrolysis side-reactions, thus enhancing the chemoselectivity of the lipase to the alcohol in comparison with water. Theoretical analysis also indicated that the time-course yield and the enantiomeric excess for the desired enantiomer could be improved if the employed lipase had higher activity and enantioselectivity for the hydrolysis and esterification side-reactions, especially when the base had a similar racemization rate compared with the rate of the fast-reaction substrate.