This paper aims to analyze the problem of ion selectivity and, in particular, sodium and chloride ions, through semi-infinite carbon nanotubes decorated by a functional group at the entry. A continuum approach is adopted to model the Van der Waals and the electrostatic interactions using the 6–12 Lennard–Jones and the Coulomb potentials, respectively. Suction energy imparted to the ion in the form of an increased velocity is determined. Moreover, an acceptance condition is obtained in the absence and the presence of functional group to examine whether the rested core is completely sucked into the nanotube or not. With respect to the proposed formulations, numerical results of suction and acceptance energies along with potential energy and interaction force distribution are presented by varying the functional group charge and nanotube radius. Unlike acceptance energy, suction energy configuration is shown to be independent of electrostatic interactions. Our numerical results also indicate that the ion selectivity can be altered by changing the sign and magnitude of functional group charge. In the presence of functional group, it is observed that the acceptance radius of a counterion always reduces and thus the ion can pass through the nanotube more easily.