A mechanistic model on catalyst deactivation by coke formation in a continuous stirred tank reactor (CSTR) has been developed in the paper. Catalyst deactivation by coke formation was treated as a surface reaction. Four reaction mechanisms representing coke formation through different routes were proposed. The evolved system of ordinary differential equations (ODEs) was solved numerically using MATLAB. This approach was validated by applying it to the skeletal isomerization of 1-pentene over ferrierite. Simulation results were compared qualitatively to those obtained from the literature. Simulation results indicated that coke formation is an extremely rapid process with fast formation of coke components on the strongest acid sites leading to final coke. The coke deposition is slower at higher residence times resulting in more stable product formation and weaker deactivation. The results obtained from this work revealed that the developed model is indeed able to successfully demonstrate the most essential features of catalyst deactivation by coke formation and are in agreement with the findings in the literature. Future work is aimed to extend the study to different reactors such as a plug flow reactor, in addition to analysis of the reaction system’s sensitivity to variables such as temperature and pressure.