Polymer electrolyte membrane fuel cells (PEMFCs) integrated into civil aircraft hold significant promise for enhancing aircraft design by reducing noise, emissions, and possibly achieving higher system efficiencies. By introducing fuel cells into electric aircrafts, strict requirements regarding reliability must be met. In this study, the impact of ionizing radiation on the degradation of a fuel cell membrane was studied. This was done by exposing the membrane electrode assembly (MEA) of the fuel cell to monoenergetic neutrons of 1.2 MeV and 14.8 MeV. These neutron energies were selected to span a relevant portion of the neutron spectrum encountered during cruise. For each energy, two neutron fluences were applied to simulate cumulative exposures equivalent to 25 000 h and 100 000 h representing the fuel cell’s target lifetime and typical aircraft service life respectively. Post-irradiation analysis revealed activation of elemental fluorine in the polymer via the 19F(n,2n)18F reaction under 14.8 MeV irradiation, whereas no comparable elemental activation was observed for the 1.2 MeV exposure within the detection limits, consistent with the fact that neutron-induced activation typically becomes significant above ~10 MeV. The next stage of this study will closely focus on quantifying how these irradiation conditions influence PEMFC performance through electrochemical characterization, complemented by scanning electron microscopy, to identify any irradiation-induced microstructural or interfacial changes in the MEA. In future work, the same irradiation protocol will be extended to lithium-ion pouch cells to assess broader implications of the aviation neutron environment for electrified aircraft energy systems.