Redox flow batteries are attractive for large-scale energy storage due to a combination of high theoretical efficiencies and decoupled power and energy storage capacities. Efforts to significantly increase energy densities by using nonaqueous electrolytes have been impeded by separators with low selectivities. Here, we report nanoporous separators based on aramid nanofibres, which are assembled using a scalable, low cost, spin-assisted layer-by-layer technique. The multilayer structure yields 5 ± 0.5 nm pores, enabling nanofiltration with high selectivity. Further, surface modifications using polyelectrolytes result in enhanced performance. In vanadium acetylacetonate/acetonitrile-based electrolytes, the coated separator exhibits permeabilities an order of magnitude lower and ionic conductivities five times higher than those of a commercial separator. In addition, the coated separators exhibit exceptional stability, showing minimal degradation after more than 100 h of cycling. The low permeability translates into high coulombic efficiency in flow cell charge/discharge experiments performed at cycle times relevant for large-scale applications (5 h).