Two fuel cell architectures, differing only by the surfaces onto which the electrodes were applied, have been analyzed to determine the root causes of dissimilarities in performance. The basic proton exchange membrane fuel cell is comprised of the proton transporting membrane, platinum-containing anode and cathode electrodes, porous carbon fiber gas diffusion media (GDM), and flow fields that deliver the reactant hydrogen and air flows. As no optimal cell design currently exists, there is a degree of latitude regarding component assembly and structure. Catalyst coated diffusion media (CCDM) refers to a cell architecture option where the electrode layers are coated on the GDM layers and then hot pressed to the membrane. Catalyst coated membrane (CCM) refers to an architecture where the electrodes are transferred directly onto the membrane. A cell with CCDM architecture has tightly bonded interfaces throughout the assembly, which can result in lower thermal and electrical contact resistances. Considering the fuel cell as a 1D thermal system, the through-plane thermal resistance was observed to decrease by 5–10% when comparing CCDM to CCM architectures. This suggests that the thermal contact resistance at the electrode interfaces was significantly reduced in the hot-press process. In addition, the electrical contact resistances between the electrode and GDM were observed to be significantly reduced with a CCDM architecture. This study shows that these effects, which have a potential to increase performance, can be attributed to the hot-press lamination process and use of CCDM architecture.