Fabrication and testing of Proton Exchange Membrane (PEM) fuel cells to improve performance is an expensive and time-consuming process. This paper presents a novel procedure for using computer simulation – namely the ANSYS PEM Fuel Cell Module – to identify key performance limiting factors in fuel cell mode of a PEM Unitised Regenerative Fuel cell (URFC) fabricated at RMIT by comparing its performance with a higher performing URFC reported in the literature. The diagnostic analysis is performed in two steps: firstly, changing operating conditions to ensure both cells are compared based on the same conditions; secondly identifying differences in cell properties, specifically catalyst exchange current densities and membrane conductivity. The simulation results show that applying the more optimal operating conditions of the higher performing cell doubled the maximum power of the RMIT cell (from 0.163 W/cm2 to 0.327 W/cm2). To overcome the remaining performance deficit in the ohmic polarization region, the value of the protonic conduction coefficient in the modelled RMIT cell had to be increased. Overall the study indicates that computer simulation modelling, in conjunction with carefully focussed experiments, can be a very useful tool in diagnosing fuel-cell performance problems.