This study develops a novel method to remove the free cations created during the synthesis of ionic liquid. The cations are removed from the ionic liquid by size-selective adsorption onto chemically surface-modified Zeolite. The porous crystal nano-structure of Zeolite has several electron-rich Al sites to attract cations. While large cations of an ionic liquid cannot access the Zeolite nano-structure, small cations like Na+ have ready access and are adsorbed. This study confirms that: Na+ can be removed from ionic liquid effectively using Zeolite; and, in contrast to the conventional and extensively applied ion exchange resin method or solvent extraction methods, this can be done without changing the nature of the ionic liquid.