Degradation tests of two phosphoric acid (PA) doped polybenzimidazole (PBI) membrane based high temperature polymer electrolyte membrane (HT-PEM) fuel cells were reported in this paper to investigate the effects of start/stop and the presence of methanol in the fuel to the performance degradation. Continuous tests with H2 and simulated reformate which was composed of H2, water steam and methanol as the fuel were performed on both single cells. 12-h-startup/12-h-shutdown dynamic tests were performed on the first single cell with pure dry H2 as the fuel and on the second single cell with simulated reformate as the fuel. Along with the tests electrochemical techniques such as polarization curves and electrochemical impedance spectroscopy (EIS) were employed to study the degradation mechanisms of the fuel cells. Both single cells showed an increase in the performance in the H2 continuous tests, because of a decrease in the oxygen reduction reaction (ORR) kinetic resistance probably due to the redistribution of PA between the membrane and electrodes. EIS measurement of first fuel cell during the start/stop test showed that the mass transfer resistance and ohmic resistance increased which can be attributed to the corrosion of carbon support in the catalyst layer and degradation of the PBI membrane. During the continuous test with simulated reformate as the fuel the ORR kinetic resistance and mass transfer resistance of both single cells increased. The performance of the second single cell experienced a slight decrease during the start/stop test with simulated reformate as the fuel.