The development of a selective, membrane-based ion separation technology may prove useful in a wide range of applications such as water treatment, battery recycling, ion specific chemical sensors, extraction of valuable metals from sea water, and bio-medical devices. In this work we show that a flashing ratchet mechanism can be used for high precision ion separation. The suggested ratchet-based ion pumps utilize a unique feature of ratchets, the frequency dependent current reversals, to drive ions with the same charge but different diffusion coefficients in opposite directions. We show that ions with a relative diffusion coefficient difference as small as 1% can be separated by driving them in opposite directions with a velocity difference as high as 1.2 mm/s. Since the pumping properties of the ratchet are determined by an electric input signal, the proposed ion pumps can pave the way for simple large-scale, fit-to-purpose selective ion separation systems.