Many reasons may cause malfunction of a proton exchange membrane fuel cell (FC) stack. Moreover, a single defect cell can affect the whole stack functioning; therefore, the localization of this cell is crucial as well as identifying the root causes for such malfunctioning. The diagnosis tool has to be nonintrusive and easy to replicate to a new FC system. This paper explores paths to achieve such monitoring based on the use of the magnetic field induced by the FC stack internal currents. Designing and using a 3-D simulation tool allows to establish a cause and effect relationship between FC defects and specific magnetic signatures. This preliminary work enables to determine the required magnetic sensor accuracy, the sensor orientation and location as well as the experimental precautions for relevant measurements.