In this study, iron magnetic nanoparticles capped with fluorescent calixarene derivatives (Fe3O4@Calix-2 and Fe3O4@Calix-3) were prepared in one-step using coprecipitation of Fe(II) and Fe(III) in basic solution. Different techniques were used to characterize the synthesized magnetic nanoparticles, such as Fourier Transform Infrared spectroscopy (FTIR), powder X-ray diffraction (XRD), vibrating sample magnetometer (VSM) and confocal microscopy. Candida rugosa was encapsulated on synthesized nanoparticles following sol-gel method. It has been observed that under the optimum conditions, the activity of encapsulated lipase (Fe3O4@Calix-2E) was 119 U/g of support which is 4.1 times more that of the encapsulated lipase without calixarene derivative (Fe3O4@E). Comparative study show that the encapsulated lipase on nanoparticles has higher thermal and operational stability than encapsulated lipase without calixarene derivative. Among these encapsulated lipase nanoparticles, Fe3O4@Calix-2 was capable of effectively catalyze hydrolysis of racemic Flurbiprofen methyl ester with high conversion of 49% and substrate enantiomeric excess (ees) of 85% at optimum pH and temperature. The efficiency of these nanoparticles was assessed by their reusability, for that after five consecutive operational uses these encapsulated lipase nanoparticles retained their conversion ratios up to 38% and 30% respectively, in the hydrolysis of (R,S)-Flurbiprofen methyl ester. The results showed that encapsulated lipases nanoparticle with calixarene moieties lead to increased activity, stability, reusability and enhanced stereoselectivity in kinetic resolution.