This paper presents an optimisation model for a general polymer electrolyte membrane (PEM) fuel cell system suitable for efficiency and size trade-offs investigation. Simulation of the model for a base case shows that for a given output power, a more efficient system is bigger and vice versa. Using the weighting method to perform a multi-objective optimisation, the Pareto sets were generated for different stack output powers. A Pareto set, presented as a plot of the optimal efficiency and area of the membrane electrode assembly (MEA), gives a quantitative description of the compromise between efficiency and size. Overall, our results indicate that, to make the most of the size-efficiency trade-off behaviour, the system must be operated at an efficiency of at least 40% but not more than 47%. Furthermore, the MEA area should be at least 3 cm2 W−1 for the efficiency to be practically useful. Subject to the constraints imposed on the model, which are based on technical practicalities, a PEM fuel cell system such as the one presented in this work cannot operate at an efficiency above 54%. The results of this work, specifically the multi-objective model, will form a useful and practical basis for subsequent techno-economic studies for specific applications.