Abstract The deployment of proton exchange membrane fuel cell (PEMFC) for aeronautic applications is a value-added energy supply alternative that not only generates useful byproducts (oxygen-depleted air, water and heat) but addresses sensitive issues such as improving health conditions of airport personnel (silent operation minimizes noise) and decreasing greenhouse gas emission (in situ zero emissions). However, the PEMFC is yet to be industrialized due to its fast degrading components. The contribution of the several start-ups and shutdowns (a PEMFC undergoes when operated in aircraft) to the degradation is not well-understood. Hence, this study seeks to explore the effects of start-up/shutdown (SU/SD) cycling on a PEMFC’s lifetime. The SU/SD cycling is incorporated with heating to 60 °C and cooling to room temperature to mimic real-life temperature changes encountered in an aircraft. The tested membrane electrode assemblies (MEAs) were characterised for performance and evolution of its components to examine the extent and nature of degradation. More than two-thirds loss of electrochemically active surface area (ECSA) of catalyst, Pt particle growth (4.71–6.41 nm) associated with Ostwald ripening and formation of PtO from adsorption of OH− by Pt–M surface were identified to be causes of the observed voltage decay at 0.196 mV h−1 rate. Hence, it is concluded that SU/SD cycling mostly affects the catalytic component of PEMFC in the aeronautic environment.