One of the major problems facing commercialization of fuel cell systems, especially polymer electrolyte membrane (PEM) fuel cell systems is cost. Various researchers have reported different system configurations which perform differently in terms of energy utilization and cost. It is therefore important to determine the best system configuration in terms of both energy utilization and cost. In this work, exergy and economic analyses of five different PEM fuel cell system configurations were carried out in order to investigate the performance of the different systems. Thermolib software was used to simulate the operation of the systems in order to obtain data for the analysis. The return on investment (ROI) and payback period were used as measures of economic performance. The results indicated that the largest exergy loss occurs in the stack (over 90%) for all systems. This is due to the chemical exergy change that occurs as a result of the chemical change that takes place in the stack. System 1 showed the highest overall exergy and energy efficiencies of 30.18% and 59.48%, respectively followed by system 3 (29.32% and 57.79%), system 4 (28.35% and 55.88%), system 2 (26.14% and 51.52%) and system 5 (24.23% and 47.77%). An improved system configuration which has a hydrogen recirculation stream without blower and makes use of the compressor expander module (CEM) was proposed and also analyzed. It was found to have an overall exergy and energy efficiencies of 31.95% and 62.97%, respectively. The ROI and payback period evaluated for all five systems as well as the proposed system were: system 1 (3.8years and 20%), system 2 (9.4years and 4%), system 3 (4.3years and 16%), system 4 (5.8years and 11%), system 5 (12.7years and 1%) and the proposed system (2.9years and 27%). In term of both energy and cost, the proposed system configuration was found to have the best performance followed by system 1, system 3, system 4, system 2 and system 5, accordingly. This study has therefore established an improved PEM fuel cell system configuration.