The enzymatic hydrolysis of the prochiral acetyl groups of pyrimidine acyclonucleoside derivatives was catalyzed effectively by lipase Amano PS from Burkholderia cepacia (BCL) to give monoacetates with a high optical purity. The stereopreference of BCL depends on the structure of the substrates. The BCL‐catalyzed hydrolysis of the unsubstituted acyclonucleoside 2‐{[2,4‐dioxo‐3,4,5,6,7,8‐hexahydroquinazolin‐1(2H)‐yl]methoxy}propane‐1,3‐diyl diacetate is enantiotopically selective (pro‐R). After the reaction, the enantiomerically pure 2‐S isomer was obtained. The additional group on the ring caused a dramatic change in the stereopreference of the enzyme‐catalyzed deacylation compared to that of the unsubstituted compound, and the reverse chiral preference was observed. The enzymatic deacylation of prochiral ester groups of acyclonucleoside analogs substituted at C‐6 and C‐8 in 2,4‐dioxo‐3,4,5,6,7,8‐hexahydroquinazoline ring led to the 2‐R isomer (pro‐S selectivity).