The dihydrazide calix[4]arene was immobilized onto sporopollenin in order to encapsulate Candida rugosa lipase (CRL) via sol-gel entrapment. The kinetic resolution of the new encapsulated lipase was investigated for enantioselective hydrolysis of racemic naproxen methyl ester and 2-phenoxypropionic acid methyl ester. The results demonstrated that the activity and enantioselectivity of the lipase were improved when the lipase was encapsulated in the presence of calix[4]arene-immobilized sporopollenin. The encapsulated lipase showed an excellent rate of enantioselectivity against the (R/S)-naproxen methyl and (R/S)-2-phenoxypropionic acid methyl esters, with E = 350 and 295, respectively, compared to the free enzyme.