Nanofiltration (NF) is an effective technology for removing per- and polyfluoroalkyl substances (PFAS), a group of emerging pollutants. However, conventional NF membranes often reject high levels of minerals, leading to low salt/PFAS selectivity. Herein, we introduce the use of continuous ionic covalent organic framework (COF) membranes as a novel approach to achieve effective PFAS removal with high selectivity. Thin TpPa-SO3H COF selective membrane layers were fabricated on polymer supports using a scalable counter-diffusion interfacial polymerization (IP) method to form thin film composite (TFC) membranes. These membranes feature a highly negative surface charge and ordered pore channels with suitable pore sizes, leading to impressive PFAS rejection rates, with over 99 % rejection for perfluorooctanesulfonic acid (PFOS) and 90–95 % rejection for perfluorooctanoic acid (PFOA) and two short-chain PFAS. Moreover, the TpPa-SO3H membranes allowed the passage of scale-forming salts, enabling selective PFAS removal with a high salt/PFAS selectivity. Furthermore, these continuous ionic COF membranes exhibited a high water permeance of 19.9–37.5 LMH/bar, outperforming commercial membranes like NF270 and other lab-made membranes.