This paper presents the evaluation of a high-temperature proton exchange membrane (HTPEM) fuel cell for different degradation mechanisms using equivalent circuit analysis. Specific consideration is given to the variation of phosphoric acid content in the polybenzimidazole membrane and the effect on the equivalent circuit. The importance of the cell assembly and operating conditions on acid migration are discussed, and it is shown how it affects performance both in the short-term and the long-term operation of the HTPEM cell. A new method is developed, whereby acid leaching can be greatly accelerated in order to quantify performance loss. The change in system parameters as a function of membrane electrode assembly acid content is investigated using electrochemical impedance spectroscopy and compared with the changes that take place for catalyst degradation, CO poisoning, and reactant starvation. It is shown, by using the equivalent circuits, that the drop in performance relating to the individual degradation mechanisms in the cell can be investigated and isolated for fault classification in online diagnostic systems. © 2014 IEEE.