Using molecular dynamics simulations, we show that a Y-junction carbon nanotube can be used to separate K⁺ and Cl⁻ ions from a KCl solution. The Y-junction nanotube is formed by connecting two smaller carbon nanotube branches of sizes (5, 5) and (6, 6) to a larger (8, 8) carbon nanotube. While uncharged (5, 5) and (6, 6) carbon nanotubes show close to zero occupancy of K⁺ and Cl⁻ ions, we show that a negatively charged (5, 5) carbon nanotube and a positively charged (6, 6) carbon nanotube can be selective to K⁺ and Cl⁻ ions, respectively. By performing molecular dynamics simulations on the entire system comprising the Y-junction carbon nanotube, the KCl solution chamber, the push plate and the receiving chamber, we show that as the electrolyte moves through the (8, 8) carbon nanotube the K⁺ and the Cl⁻ ions can be selectively transported through the (5, 5) and the (6, 6) carbon nanotube, respectively. The formation of ion pairs can affect the separation efficiency and we discuss the conditions under which perfect separation can be obtained.