A proton exchange membrane (PEM) fuel cell has many distinctive features which make it an attractive alternative clean energy source. Some of those features are low start-up, high power density, high efficiency and remote applications. In the present study, a numerical investigation was conducted to analyse the flow field and reactant gas distribution in a PEM fuel cell channel with transversely inserted pin fins in the channel flow aimed at improving reactant gas distribution. A fin configuration of small hydraulic diameter was employed to minimise the additional pressure drop. The influence of the pin fin parameters, the flow Reynolds number, the gas diffusion layer (GDL) porosity on the reactant gas transport and the pressure drop across the channel length were explored. The parameters examined were optimized using a mathematical optimization code integrated with a commercial computational fluid dynamics code. The results obtained indicate that a pin fin insert in the channel flow considerably improves fuel cell performance and that optimal pin fin geometries exist for minimized pressure drop along the fuel channel for the fuel cell model considered. The results obtained provide a novel approach for improving the design of fuel cells for optimal performance.