Compositional proton-conducting membranes based on perfluorinated Aquivion®-type copolymers modified by detonation nanodiamonds (DND) with positively charged surfaces were prepared to improve the performance of hydrogen fuel cells. Small-angle neutron scattering (SANS) experiments demonstrated the fine structure in such membranes filled with DND (0–5 wt.%), where the conducting channels typical for Aquivion® membranes are mostly preserved while DND particles (4–5 nm in size) decorated the polymer domains on a submicron scale, according to scanning electron microscopy (SEM) data. With the increase in DND content (0, 0.5, and 2.6 wt.%) the thermogravimetric analysis, potentiometry, potentiodynamic, and potentiotatic curves showed a stabilizing effect of the DNDs on the operational characteristics of the membranes. Membrane–electrode assemblies (MEA), working in the O2/H2 system with the membranes of different compositions, demonstrated improved functional properties of the modified membranes, such as larger operational stability, lower proton resistance, and higher current densities at elevated temperatures in the extended temperature range (22–120 ◦C) compared to pure membranes without additives.