Sustainable growth and development in a society requires energy supply that is efficient, affordable, readily available and, in the long term, sustainable without causing negative societal impacts, such as environmental pollution and its attendant consequences. In this respect, proton exchange membrane (PEM) fuel cells offer a promising alternative to existing conventional fossil fuel sources for transport and stationary applications due to its high efficiency, low-temperature operation, high power density, fast start-up and its portability for mobile applications. However, to fully harness the potential of PEM fuel cells, there is a need for improvement in the operational performance, durability and reliability during usage. There is also a need to reduce the cost of production to achieve commercialisation and thus compete with existing energy sources. The present study has therefore focused on developing novel approaches aimed at improving output performance for this class of fuel cell. In this study, an innovative combined numerical computation and optimisation techniques, which could serve as alternative to the laborious and time-consuming trial-and-error approach to fuel cell design, is presented. In this novel approach, the limitation to the optimal design of a fuel cell was overcome by the search algorithm (Dynamic-Q) which is robust at finding optimal design parameters. The methodology involves integrating the computational fluid dynamics equations with a gradient-based optimiser (Dynamic-Q) which uses the successive objective and constraint function approximations to obtain the optimum design parameters. Specifically, using this methodology, we optimised the PEM fuel cell internal structures, such as the gas channels, gas diffusion layer (GDL) - relative thickness and porosity - and reactant gas transport, with the aim of maximising the net power output. Thermal-cooling modelling technique was also conducted to maximise the system performance at elevated working temperatures. The study started with a steady-state three-dimensional computational model to study the performance of a single channel proton exchange membrane fuel cell under varying operating conditions and combined effect of these operating conditions was also investigated. From the results, temperature, gas diffusion layer porosity, cathode gas mass flow rate and species flow orientation significantly affect the performance of the fuel cell. The effect of the operating and design parameters on PEM fuel cell performance is also more dominant at low operating cell voltages than at higher operating fuel cell voltages. In addition, this study establishes the need to match the PEM fuel cell parameters such as porosity, species reactant mass flow rates and fuel gas channels geometry in the system design for maximum power output. This study also presents a novel design, using pin fins, to enhance the performance of the PEM fuel cell through optimised reactant gas transport at a reduced pumping power requirement for the reactant gases. The results obtained indicated that the flow Reynolds number had a significant effect on the flow field and the diffusion of the reactant gas through the GDL medium. In addition, an enhanced fuel cell performance was achieved using pin fins in a fuel cell gas channel, which ensured high performance and low fuel channel pressure drop of the fuel cell system. It should be noted that this study is the first attempt at enhancing the oxygen mass transfer through the PEM fuel cell GDL at reduced pressure drop, using pin fin. Finally, the impact of cooling channel geometric configuration (in combination with stoichiometry ratio, relative humidity and coolant Reynolds number) on effective thermal heat transfer and performance in the fuel cell system was investigated. This is with a view to determine effective thermal management designs for this class of fuel cell. Numerical results shows that operating parameters such as stoichiometry ratio, relative humidity and cooling channel aspect ratio have significant effect on fuel cell performance, primarily by determining the level of membrane dehydration of the PEM fuel cell. The result showed the possibility of operating a PEM fuel cell beyond the critical temperature ( 80„aC), using the combined optimised stoichiometry ratio, relative humidity and cooling channel geometry without the need for special temperature resistant materials for the PEM fuel cell which are very expensive. In summary, the results from this study demonstrate the potential of optimisation technique in improving PEM fuel cell design. Overall, this study will add to the knowledge base needed to produce generic design information for fuel cell systems, which can be applied to better designs of fuel cell stacks.