Structural alterations to amorphous poly(ether ether ketone) (PEEK) produced by ion irradiation (11.2 MeV H+ and 25.6 MeV He2+ ions) were investigated by dielectric relaxation spectroscopy. The analysis in terms of the Havriliak–Negami (HN) equation and the scaling model showed an increase in the intermolecular correlation with increasing irradiation dose. The dynamic fragility index (m) was estimated from Vogel–Fulcher–Tammann analysis. Ion irradiation not only elevated the glass-transition temperature (Tg) but interestingly decreased m of the PEEK chains around Tg. This was due to increasing polar interaction and better packing efficiency of the irradiated samples compared with those of amorphous PEEK. The average size of the cooperative rearranging region decreased in line with decreasing m and indicated an increase in the rigid amorphous phase fraction after irradiation. The analysis of the direct-current conductivity confirmed that there was a strong coupling between the macroscopic ion transport and concerted segmental motion. © 2013 Wiley Periodicals, Inc. J. Appl. Polym. Sci., 2014, 131, 39929.