Structural changes produced by irradiation have been extensively studied in compounds derived from the parent fluorite structure where cations are initially ordered and in systems where both sub-lattices do not display long-range order. The irradiation behaviour of fluorite-related oxide systems where the cations are randomly distributed but the anions are highly ordered is not quantitatively explored yet. We report on a model system Gd2Ce2O7, with a randomly occupied cation sub-lattice while an ordered anion sublattice. This compound crystallizes in a new bixbyite-type symmetry where O vacancies order on half of the vacant sites of the ideal bixbyite structure. Swift heavy ion irradiation experiments and quantitative x-ray diffraction analysis were used to study the separate response of the anion sub-lattice to radiation. We show that the topological disorder on the anion sub-lattice grows faster than that on the cation sub-lattice. While a decrease in strain is observed as a function of fluence, the variance of the strain increases due to an increase of the microdomain wall density.