In this study, we investigated the influence of the Catalyst-Layer (CL) structure on Polymer Electrolyte Fuel Cell (PEFC) performance using an inkjet coating printer, and we especially focused on the CL thickness and the electrode area. In order to evaluate the influence of CL thickness, we prepared four Membrane Electrode Assemblies (MEAs), which have one, four, five and six CLs, respectively, and evaluated it by an overpotential analysis. As a result, the overpotentials of an activation and a diffusion increased with the increase of thickness of CL. From Energy Dispersive X-ray spectroscopy (EDX) analysis, because platinum twines most ionomers and precipitates, the CL separates into a layer of platinum with a big grain aggregate ionomer and the mixing layer of platinum and ionomer during the catalyst ink drying process. Consequently, the activation overpotential increased because the three-phase interface was not able to be formed sufficiently. The gas diffusivity of the multilayer catalyst electrode was worse than that of a single layer MEA. The influence of the electrode area was examined by two MEAs with 1 and 9 cm2 of electrode area. As a result, the diffusion overpotential of 9 cm2 MEA was worse than 1 cm2 MEA. The generated condensate was multiplied and moved to the downstream side, and thereafter it caused the flooding/plugging phenomena.