The world's pollution rates have been increasing exponentially due to the many reckless lifestyle practices of human beings as well as their choices of contaminating power sources. Eventually, this lead to a worldwide awareness on the risks of those power sources, and in turn, a movement towards the exploration and deployment of several green technologies emerged. Proton Exchange Membrane Fuel cells (PEMFCs) are one of those green technologies. However, in order to be able to successfully and efficiently deploy PEMFC systems, a solid fault diagnosis scheme is needed. The development of accurate model based fault diagnosis schemes has been imposing a lot of challenge and difficulty on researchers due to the high complexity of the PEMFC system. Furthermore, confidentiality issues with the manufacturer can also impose further constraints on the model development of a commercial PEMFC system. In this work, an approach to develop an accurate PEMFC system model despite the lack of crucial system information is presented through the use of Siemens LMS AMESim software. The developed model is then used to develop a fault diagnosis scheme that is able to detect and isolate five system faults.