One of the most important applications of cyclic peptide nanotubes (CPNTs) is their potential to be used as artificial ion channels. Natural ion channels are large and complex membrane proteins, which are very expensive, difficult to isolate, and sensible to denaturation; for this reason, artificial ion channels are an important alternative, as they can be produced by simple and inexpensive synthetic chemistry paths, allowing manipulation of properties and enhancement of ion selectivity properties. Artificial ion channels can be used as component in molecular sensors and novel therapeutic agents. Here, the electrophoretic transport of Na+ and K+ ions within cyclic peptide nanotubes is investigated by using molecular dynamic simulations. The effect of electric field in the stability of peptide nanotubes was studied by calculating the root mean square deviation curves. Results show that the stability for CPNTs decreases for higher electric fields. Selective transport of cations within the hydrophilic tubes was observed and the negative Cl- ions did not enter the peptide nanotubes during the simulation. Radial distribution functions were calculated to describe structural properties and coordination numbers and changes in the first and second hydration shell were observed for the transport of Na+ and K+ inside of cyclic peptide nanotubes. However, no effect on coordination number was observed. Diffusion coefficients were calculated from the mean square deviation curves and the Na+ ion showed higher mobility than the K+ ion as observed in equivalent experimental studies. The values for diffusion coefficients are comparable with previous calculations in protein channels of equivalent sizes.