The automated process of coating catalyst layers on gas diffusion electrodes (GDEs) for high-temperature proton exchange membrane fuel cells results inherently into a number of defects. These defects consist of agglomerates in which the platinum sites cannot be accessed by phosphoric acid and which are the consequence of an inconsistent coating, uncoated regions, scratches, knots, blemishes, folds, or attached fine particles—all ranging from μm to mm size. These electrochemically inactive spots cause a reduction of the effective catalyst area per unit volume (cm2/cm3) and determine a drop in fuel cell performance. A computational fluid dynamics (CFD) model is presented that predicts performance variation caused by manufacturing tolerances and defects of the GDE and which enables the creation of a six-sigma product specification for Advent phosphoric acid (PA)-doped polybenzimidazole (PBI)-based membrane electrode assemblies (MEAs). The model was used to predict the total volume of defects that would cause a 10% drop in performance. It was found that a 10% performance drop at the nominal operating regime would be caused by uniformly distributed defects totaling 39% of the catalyst layer volume (~0.5 defects/μm2). The study provides an upper bound for the estimation of the impact of the defect location on performance drop. It was found that the impact on the local current density is higher when the defect is located closer to the interface with the membrane. The local current density decays less than 2% in the presence of an isolated defect, regardless of its location along the active area of the catalyst layer.