Pr2NiO4+δ oxide with a layered Ruddlesden–Popper structure is a promising material for SOFC cathodes and oxygen separation membranes due to a high oxygen mobility provided by the cooperative mechanism of oxygen migration involving both interstitial oxygen species and apical oxygen of the NiO6 octahedra. Doping by Ca improves thermodynamic stability and increases electronic conductivity of Pr2 − xCaxNiO4+δ, but decreases oxygen mobility due to decreasing the oxygen excess and appearing of 1–2 additional slow diffusion channels at x ≥ 0.4, probably, due to hampering of cooperative mechanism of migration. However, atomic-scale features of these materials determining oxygen migration require further studies. In this work characteristics of oxygen diffusion in Pr2 − xCaxNiO4+δ (x = 0–0.6) are compared with results of the surface analysis by X-ray photoelectron spectroscopy and modeling of the interstitial oxygen migration by the plane-wave density functional theory calculations. According to the X-ray photoelectron spectroscopy data, the surface is enriched by Pr for undoped sample and by Ca for doped ones. The O1s peak at ~531 eV corresponding to a weakly bound form of surface oxygen located at Pr cations disappears at ~500 °C. Migration of interstitial oxygen was modeled for a I4/mmm phase of Pr2NiO4+δ. The interstitial oxygen anion repulses the apical one in the NiO6 octahedra pushing it into the tetrahedral site between Pr cations. The calculated activation barrier of this migration is equal to 0.585 eV, which reasonably agrees with the experimental value of 0.83 eV obtained by the oxygen isotope exchange method. At the same time, for the model compound Ca2NiO4+δ, obtained by isomorphic substitution of Pr by Ca in Pr2NiO4+δ, calculations implied formation of the peroxide ion comprised of interstitial and lattice oxygen species not revealed in the case of incomplete substitution (up to PrCaNiO4+δ composition). Hence, calculations in the framework of the plane-wave density functional theory provide a realistic estimation of specificity of oxygen migration features in Pr2NiO4+δ doped by alkaline-earth metals.