Perfluorosulfonic acid (PFSA) ionomers are ubiquitous as proton-exchange membranes (PEMs) in vanadium redox flow batteries (VRFBs), as they provide high proton conductivity and robust chemical stability. However, traditional PFSA ionomers suffer from high vanadium ion crossover, i.e., low ion selectivity, which reduces the efficiency and lifetime of the battery. Herein, a novel method to fabricate PFSA nanocomposites containing fluorocarbon-decorated silica nanoparticles is presented. These composite ionomers exhibit drastically reduced vanadium ion permeability and an almost two orders of magnitude increase in proton selectivity when compared to the current benchmark commercial ionomer. Small-angle neutron scattering data suggest that the nanostructures of these nanocomposites are drastically different from their pristine counterpart, where the periodic spacing of the hydrophobic domains is significantly reduced, while changes to the ionic structure were seen to be minimal. This work suggests that composite PEMs containing a secondary phase that alters the hydrophobic, nonion-conducting phase of the ionomer may prove to be a fruitful fabrication route to produce ionomer membranes with enhanced performance for use in VRFBs.