In this study, quantum mechanical calculations have been performed to systematically analyse two different reaction mechanisams for the skeletal isomerisation of cis-butene to isobutene in ferrierite zeolite. One involves a conventional mechanism that proceeds via stable alkoxide intermediates and the other one which proceeds via carbenium ions only. The calculations were performed using 27T quantum mechanical cluster model representations of ferrierite, which is described using the M062X density functional. Although the carbenium ion structures formed over the pathway are inherently less stable than the alkoxide intermediates formed in the conventional mechanism, the rate determining step is predicted to be almost 10 kcal/mol lower in energy. The higher barrier for the latter process is due to the inherent stability of the intermediates formed within the pore. This appears to suggest that while these intermediates are formed over the course of a reaction, the skeletal isomerisation of butenes in ferrierite only occurs via a carbenium based mechanism. This proposal is consistent with experimental results that alkoxide intermediates are experimentally observed species.