The effect of the catalyst microstructure on a 5 cm 2 PEM fuel cell performance is numerically investigated. The catalyst layer composition and properties (i.e. ionomer volume fraction, platinum loading, particle radius, electrochemical active area and carbon support type), and the mass transport resistance due to the ionomer and liquid water surrounding the catalyst particles, are incorporated into the model. The effects of the above parameters are discussed in terms of the polarization curves and the local distributions of the key parameters. An optimum range of the ionomer volume fraction was found and a gain of 39% in the performance was achieved. As regards the platinum loading and catalyst particle radius, the results showed that a higher loading and a smaller radius leads to an increase in the PEMFC performance. Further, the influence of the electrochemical active area produces an overall increase of 22% in current density and this was due to the use of a new material developed as support for Pt particles, an iodine doped graphene, which has better electrical contacts and additional pathways for water removal. Using this parameter, the numerical model has been validated and good agreement with experimental data was achieved, thus giving confidence in the model as a design tool for future improvements of the catalyst structure.