Vanadium redox flow battery (VRFB) is a very promising solution for large‐scale energy storage, but some technical issues need to be addressed. Crossover, i.e., the undesired permeation of vanadium ions through the cell separator, causes capacity loss and self‐discharge. Low‐cost and highly selective separators are thus required to improve the competitiveness of this technology. This work investigates the use of silica nanoparticles in an innovative selective layer to improve membrane selectivity and reduce its thickness. 1.5 μm thick barrier layers composed of 1100EW Nafion ionomer with silica (≈3–13 nm diameter) and Vulcan XC‐72R (≈40 nm) nanoparticles in different proportions are directly deposited on 50 μm thick Nafion membranes. The barrier layer composed only of silica nanoparticles reduces the self‐discharge due to crossover by 5 times and increases the average efficiency of the battery. Finally, during more than 1000 h of operation, the barrier layer on a 25 μm Nafion membrane demonstrates excellent stability, working with a constant coulombic efficiency higher than 99% and a capacity decay rate comparable with a thicker Nafion membrane, thus enabling the use of thinner membranes in VRFB, allowing an estimated 8% stack costs reduction with respect to NR212.