The recent development of electric vehicles and electronic equipment has resulted in a demand for portable power supply systems with high power density and life expectancy. High Temperature (HT) Proton Exchange Membrane (PEM) fuel cells have emerged as a possible solution to this requirement. Recent advances in the materials allow the cells to operate at higher temperatures resulting in a number of advantages. These systems still suffer from degradation mechanisms that can degrade performance and decrease the life expectancy. In order to diagnose the fuel cell performance and degradation mechanisms, impedance analysis can be performed. This paper presents a design for the power electronic hardware that can perform these analyses online for single cell applications, where the output voltage is very low. Special consideration must be given to the hardware selection and small signal injection capability. The Nyquist plots and small amplitude current step voltage response of the HTPEM fuel cell is presented along with those captured after catalyst degradation has occurred. It is shown how the online system can capture these changes by using equivalent circuits. © 2013 IEEE.