An electrochemical hydrogen pump (EHP) with a proton exchange membrane (PEM) used as part of fusion cycle systems successfully combines the processes of hydrogen extraction, purification and compression in a single device. This work comprises a novel study of the effect of ionizing radiation on the properties of the PEM as part of the EHP. Radiation exposure leads to nonspecific degradation of membranes, changes in their structure, and destruction of side and matrix chains. The findings from this work reveal that the replacement of sulfate groups in the membrane structure with carboxyl and hydrophilic groups leads to a decrease in conductivity from 0.115 to 0.103 S cm−1, which is reflected in halving the device performance at a temperature of 30 °C. The shift of the ionomer peak of small-angle X-ray scattering curves from 3.1 to 4.4 nm and the absence of changes in the water uptake suggested structural changes in the PEM after the irradiation. Increasing the EHP operating temperature minimized the effect of membrane irradiation on the pump performance, but enhanced membrane drying at low pressure and 50 °C, which caused a current density drop from 0.52 to 0.32 A·cm−2 at 0.5 V.