The dynamic mechanical relaxation of non-crystalline poly(aryl ether-ether-ketone) PEEK and the one irradiated with electron beam were studied. The three distinct γ, β, α′ relaxation maxima were observed in unirradiated PEEK from low to high temperature. It was revealed from the study on the irradiation effects that three different molecular processes are overlapped in γ relaxation peak, i.e., molecular motion of water bound to main chain (peak temperature; at −100°C), local motion of main chain (at −80°C), and local mode of the aligned and/or oriented moiety (at −40°C). The β relaxation connected with the glass transition occurred at 150°C and it shifted to higher temperature by irradiation. The α′ relaxation which can be attributed to rearrangement of molecular chain due to crystallization was observed in unirradiated PEEK ∼ 180°C and its magnitude decreased with the increase in irradiation dose. This effect indicates the formation of structures inhibiting crystallization such as crosslinking and/or short branching during irradiation. A new relaxation, β′, appeared in the temperature range of 40° to 100°C by irradiation and its magnitude increased with dose. This relaxation was attributed to rearrangement of molecular chain from loosened packing around chain ends, which were introduced into the non-crystalline region by chain scission under irradiation, to more rigid molecular packing, From these observations, we proposed that deterioration in mechanical properties of non-crystalline PEEK by high energy electron beam was brought about not only by chain scission but structural changes such as crosslinking and/or branching in the main chain.