Wastewater treatment plants help removing organic matter from wastewater, and at the same time, generate digester gas as a useful byproduct. Digester gas is rich in methane, which can be used to generate electricity. Fuel cell systems are the cleanest technology for power recovery from digester gas, since all other technologies generate electricity by burning all the digester gas. The most commonly used type of fuel cell for power generation from digester gas in wastewater treatment plants is the molten carbonate fuel cell. This type of fuel cell can tolerate the impurities usually found in digester gas, such as CO2 and H2S; however, this kind of fuel cell systems is more suitable for large wastewater treatment plants. This prevents the use of fuel cells for power generation from digester gas in wastewater treatment plants serving medium and small size cities, or even farms. This research attempts to explore solutions to make fuel cell technologies technically and economically feasible for medium and small size wastewater treatment plants. The most suitable type of fuel cells for small applications is the Proton Exchange Membrane, PEM, fuel cell. The main challenge in using PEM fuel cells for power recovery from digester gas is that they are highly sensitive to impurities in its hydrogen gas supply. Therefore, in order to use PEM fuel cells in this application, energy must be spent in cleaning the digester gas before it enters the PEM fuel cell and reformer system. Energy is also required in the form of heat by the reformer system to produce the hydrogen needed by the fuel cell. Both the energy used in the cleaning of the digester gas and the hydrogen generation process comes from burning part of the digester gas. This reduces the amount of digester gas available for hydrogen production and electricity generation, respectively. The approach followed in this investigation seeks to develop a Simulink® model of the reformer and fuel cell so that the modeling tools of Matlab® can be used to simulate the performance of the system under different operating conditions. A sensitivity analysis is carried out to identify critical operating parameters affecting the performance of the overall system. The results obtained in this work provide guidelines for future studies of performance optimization and optimal control using the tools available in Matlab®, in order to get maximum electricity generation from digester gas using PEM fuel cell systems.