Hydrophilicity is critical in Nafion membranes during fuel cell operation as insufficient membrane hydration leads to brittle behavior and a drop in proton conductivity. The incorporation of APTS (3-(aminopropyl)triethoxysilane) into exfoliated graphene oxide (EGO) by covalent functionalization to be used as filler into Nafion membranes allows higher hydrophilicity for these membranes. This is associated with promoting hydroxyl, carbonyl, siloxane, silane, and amine groups within the EGO-APTS matrix. The incorporation of these materials as Fuel Cell MEAs leads to a significant reduction of the ohmic resistance measured at high frequency resistance (HFR) in electrochemical impedance spectroscopy (EIS) experiments and achieves maximum power densities of 1.33 W cm−2 at 60 °C at 100% RH (APTS-EGO, 0.2 wt%) and 1.33 W cm−2 at 60 °C at 70% RH (APTS-EGO, 0.3 wt%), which represents an improvement of 190% compared to the commercial Nafion 212 when utilizing low humidification conditions (70%). Moreover, the as-synthesized membrane utilizes lower Nafion ionomer mass, which, in conjunction with the excellent cell performance, has the potential to decrease the cost of the membrane from 87 to 80 £/W as well as a reduction of fluorinated compounds within the membrane.