This work presents the synthesis of new mercapto calix[4]arenes derivatives (4 and 5). These derivatives were capped on Fe3O4 magnetic nanoparticles and subsequently encapsulated with Candida rugosa through sol-gel method to furnish enc-4 and enc-5, respectively, to enhance catalytic activity and enantioselectivity of lipase for hydrolysis reaction of racemic flurbiprofen methyl ester. Catalytic activity and enantioselectivity of enc-4 and enc-5 were assayed at different pH and temperature conditions and it was found that the resultant encapsulated enzyme exhibited higher thermal and operational stabilities compared to the free lipasein which enc-5 showed the excellent rate of enantioselectivity (E=176) for S-flurbiprofen better than free lipase (E=137) at pH 7 and 35°C for 48h. The time study shows that enantioselectivity reached the maximumvalue of E=244 after 72h. Catalytic activity of these materials was hardly affected by 20 and 23% after five usages of enc-4 and enc-5, respectively.