Skeletal isomerization of I-butene to isobutene has been investigated over various metal-cation-exchanged natural clinoptilolite zeolites. The effects of metal cation exchange were examined by XRD, NH3-TPD, FT-IR, and solid-state NMR to elucidate the controlling factors affecting the selectivity to isobutene. Cobalt-cation-exchanged natural clinoptilolite zeolite (Co-HNZ) showed a higher selectivity to isobutene compared with that of HNZ at the same conversion of n-butenes under the same reaction conditions, while barium-cation-exchanged zeolite (Ba-HNZ) exhibited a higher activity but a very low selectivity to isobutene. It could be suggested that the high selectivity over the Co-HNZ catalyst was induced by selective removal of strong acid sites that were responsible for the side reactions of dimerization cracking as well as by imposing an effective constraint on zeolite channels. On the other hand, the high density and easy accessibility of acid sites mainly on the external surface in Ba-HNZ could increase the extent of the bilmolecular reaction pathway, leading to high yields of by-products. Thus, a selective catalyst for skeletal isomerization of 1-butene should satisfy multiple requirements regarding its acid site, namely, strength, type, concentration, and accessibility.