Identifying the location of the active sites in a zeolite is a current challenge, impeding the design of optimal catalysts. In this work, we identify the location of the most active sites of 1-ethylcyclohexene isomerization in the EUO framework (10 MR channels, 12 MR side pockets), thanks to DFT calculations corroborated by experiments. Skeletal isomerization of cycloalkenes is a crucial industrial reaction for the bifunctional isomerization of ethylbenzene. Ethylcyclohexene is protonated by framework protons into cyclic carbenium ions, which undergo ring contraction-expansion reactions through protonated cyclopropane (PCP) like transition states. Ab initio calculations clearly show that the acid sites located at the intersection between the channel and the pocket stabilize much less the cyclic carbenium ions involved in the reaction than 12 MR pockets and 10 MR channel sites, due to stronger dispersion stabilizing interactions. This computational finding is fully confirmed experimentally by the comparison of the catalytic performances of the H-EU-1 and H-ZSM-50 zeolites in ethylcyclohexane hydroisomerization. Both zeolites possess the EUO structure, but with different location of the acid sites. The ratio in turnover frequencies is quantitatively rendered by the DFT calculated free energy profiles. Diffusion measurements reveal similar ethylcyclohexane diffusion times for the two zeolites, supporting that the difference in activity is primarily driven by the location of the active sites.