The proton form of the natural clinoptilolite zeolite (HNZ) was modified by treatment with various acids. Effects of modification on catalytic performance were investigated for the skeletal isomerization of n-butenes to isobutene. Among HNZs treated with various acids, only those modified with boric acid (B-HNZ) showed an improved catalytic performance of skeletal isomerization in terms of activity and stability. Furthermore, B-HNZ exhibited higher isobutene selectivity compared to unmodified HNZ at the same conversion of n-butenes. The performance was comparable to that of a widely known ferrierite catalyst at the same reaction conditions. The main effect of boric acid treatment on HNZ was the selective increase in the number of acid sites of moderate strength required for efficient catalysts in skeletal isomerization without collapse of its framework. These acid sites of moderate strength were considered to be selective and stable reaction sites for skeletal isomerization of n-butenes. Coke deposition poisoned non-selective strong acid sites and imposed a spatial restriction on zeolite channels, leading to suppression of undesired dimerization reactions. Factors affecting selectivity to isobutene an discussed.