A polymer electrolyte membrane fuel cell (PEMFC) is one of the promising renewable energy conversion systems; however, its performance is considerably limited by the sluggish transport properties and/or reaction kinetics of the catalyst layers, especially at a high current density. In this study, graphene-based, thin Nafion (R) membranes are prepared using 0 to 4wt% of graphene nanoflakes, and the effects of the graphene are examined for enhanced transport properties. The electrical conductivity and dielectric constant are drastically enhanced to 0.4 mS/cm and 26 at 4 wt% of graphene nanoflakes, respectively, while the thermal conductivity linearly increases to 3 W/m-K. The proton conductivity also significantly increases with the aid of graphene nanoflakes at >2 wt% of graphene nanoflakes, and the enhancement doubles compared with those of the carbon-black (CB)-based and carbon nanotube (CNT)-based, thin Nafion (R) membranes, perhaps due to unique graphene structures. Additionally, the quasi-steady-state water contact angle increases from 113 degrees to similar to 130 degrees with the addition of graphene nanoflakes, showing that a hydrophobic-like water wetting change may be related to the significant proton conductivity enhancement. This work provides an optimal material design guideline for the transport-enhanced cathode catalyst layer using graphene-based materials for polymer electrolyte membrane fuel cell applications.