Catalytic deactivation caused by coking was studied in zeolite Y and ZSM5 during 1-hexene isomerization under subcritical and supercritical conditions. The effects of varying temperature and pressure, from 220 to 250 °C and from 10 to 70 bar, respectively, on conversion and coke deposition were studied in both zeolites. Thermogravimetric analysis (TGA) data, diffuse reflectance infrared Fourier transform spectra (DRIFTS), and nitrogen sorption isotherms for fresh and coked catalysts were compared. In zeolite Y an exponential decay in conversion was observed with the rate of deactivation being slower at supercritical conditions at 235 °C and 40 bar than subcritical conditions at 235 °C and 10 bar. It is thought that in zeolite Y the micropores with diameter 7.4 Å could accommodate coke molecules leading to the observed deactivation; however, in ZSM5 the micropores of 5.3–5.6 Å diameter were too small to accommodate coke molecules, and thus coke was deposited outside the zeolite crystals within the mesopores of the alumina binder. Although zeolite Y deactivated, while ZSM5 did not, the use of a supercritical fluid reaction environment enabled the conversion at 235 °C, 40 bar to be maintained at 42% over zeolite Y, which was higher than the conversion of 34% over ZSM5 catalyst under the same conditions. Operating with supercritical fluid led to the partial alleviation of the significant coking effects observed with zeolite Y and improved its viability for use in this reaction compared with the performance of ZSM5.