Exergy and economic analysis is often used to find and identify the most efficient process configuration for proton exchange membrane fuel cell from the thermo-economic point of view. This work gives an explicit account of the synergetic effect of exergetic and economic analysis of proton exchange membrane fuel cell (PEMFC) using methanol and methane as fuel sources. This was carried out through computer simulation using Thermolib simulation toolbox. Data generated from the simulated model were subsequently used for the thermodynamic and economic analysis. Analysis of energy requirement for the two selected processes revealed that the methane fuelled system requires the lower amount of energy (4.578 kJ/s) in comparison to the methanol fuelled configuration which requires 180.719 J/s. Energy analysis of both configurations showed that the principle of energy conservation was satisfied while the result of the exergy analysis showed high exergetic efficiency around major equipment (heat exchangers, compressors and pumps) of methane fuelled configuration. Higher irreversibility rate were observed around the burner, stack, and steam reformer. These trends of exergetic efficiency and irreversibility rate were observed around equipment in the methanol fuelled system but with lower performance when compared with the methane fuelled process configuration. On the basis of overall exergetic efficiency and lost work, the methanol system was more efficient with lower irreversibility rate of 547.27 kJ/s and exergetic efficiency of 34.44% in comparison with the methane fuelled system which has the highest irreversibility rate of 624.03 kJ/s and highest exergetic efficiency of 36.51%. Economic analysis showed that methane system had a lower capital cost of $ 476 396.2 and slightly higher annual utility cost of $ 10 334.2 as against the methanol system whose capital and annual total utility cost were $ 683 919 and $ 10 073 respectively. The methane system configuration is favoured based on the assumed economic parameters by the least cost per kilowatt of electricity produced ($3 804.99/kW). The result of various analysis conducted shows that trade-off between economic, energy and exergetic performance of methane and methanol system favoured selection of methane system configuration as the best preferred choice of PEMC configuration. (c) 2016 Elsevier Ltd. All rights reserved.