The mobility of the pentane isomers in the hydroxylated UiO-66 metal-organic framework has been characterized. 2H NMR spectroscopy was applied to measure the jump rate of alkanes guest molecules between adjacent cages and estimate the diffusivity. It is inferred that the difference in diffusion coefficients defines the kinetic separation selectivity, which is higher for the linear alkanes. The adsorption of pentane isomers in UiO-66 has been modeled with molecular dynamics (MD) simulation. The adsorbed quantity of isopentane is higher than that for n-pentane, providing the possibility of separation with selectivity α ≈ 8 in stationary conditions. The impact of the UiO-66 MOF hydroxylation state on the mobility of pentane isomers has been characterized by comparison with results obtained for the dehydroxylated UiO-66 material. The hydroxylated state of UiO-66 MOF has 6-time higher separation selectivity for pentane isomers compared to its dehydroxylated state (αhyd ≈ 76). MD calculations show that hydroxylated UiO-66 MOF is more efficient, as the separation selectivity is 4 times lower in the dehydroxylated material. The UiO-66 hydroxylation effect is compared for the mobility of C4 and C5 alkanes. The optimal conditions for C4/C5 alkanes kinetic separation by UiO-66 MOF are established.