The main objective of this study is to introduce the short cut design method for the conceptual design of a proton electrolyte of membrane fuel cell (PEMFC) system. Initially, as a model development of the system, this paper tends to focus on the overall system design of the fuel cell. Basically, the system consist of five major units, namely; Auto-thermal reformer (ATR), water gas shift reactor (WGS), membrane, pressure swing adsorber (PSA) and fuel cell stack. The ATR and WGS are designed based on the rate of reaction and variations in volume. For membrane unit, the expression of the length and surface area are simplified in terms of NTU and HTU. The PSA process is quite complicated and there are many parameters to be decided; therefore, we simplify the design of the PSA by introducing Daud bed utilisation factor. For the stack design, the voltage for single cell, number of cells required, current density, power density and finally the current flow in the stack are determined in this study. The material and heat balance of the system are also presented here. Finally the overall fuel cell efficiency is also determined. System with power output as 5 kW of PEMFC is taken as a case study. Methanol is taken as a primary fuel source to the ATR system, which is fed together with steam and oxygen. The conceptual design indicates that if the mole ratio of O-2/MeOH is 0.20-0.25, then the hydrogen selectivity is around 2.5-2.6 for complete methanol conversion. With that the ratio of MeOH:H2O and MeOH:O-2 are taken as 1:1.3 and 1:0.25, respectively. The conceptual design also proves that WGS reaction plays a very important role in the reduction of the CO produced in the ATR. In the conceptual design, the ATR product contains H-2: 73%, CO: 2%, and CO2: 25%. The CO level is then further reduced to less than 2000 ppm in the WGS reactor. Hydrogen-rich reformate, which is produced by reforming primary fuels in the fuel processor system contains significant amount of CO, is further reduced by tubular ceramic membrane (TCM) and a pressure swing adsorber (PSA) in series. From the overall material balance, it is observed that the final concentration of hydrogen is purified to 99.99% with the concentration of CO is reduced to less than 10ppm before entering the fuel cell stack. Finally this paper will calculate the overall heat balance of the system in order to calculate the power plant efficiency. The gross efficiency of the system is calculated as 49.3% while the net efficiency of the system after considering the parasitic load is estimated as 45.5%. (C) 2004 Elsevier B.V. All rights reserved.