A-site deficient Ruddlesden–Popper phases now attract a lot of attention as promising materials for intermediate temperature solid oxide fuel cells' cathodes and oxygen separation membranes. However, controversial information on the A-site deficiency effect on structural, transport and electrochemical properties of these materials apparently requires further studies of such systems. In this work, structural and transport features of (Nd2-xCax)0.975NiO4+δ system were studied. (Nd2-xCax)0.975NiO4+δ (x = 0–0.4) samples were synthesized via a solution-assisted solid state reaction method and characterized by X-ray diffraction. Oxygen transport was studied by the temperature programmed isotope exchange of oxygen with C18O2 in the flow reactor. A high oxygen mobility of materials (D* ~ 10−7 cm2/s at 700 °C) is provided by the cooperative mechanism of oxygen migration involving both regular and highly-mobile interstitial oxygen. As typical for Ruddlesden–Popper phases, doping with Ca leads to increase of total conductivity due to holes' formation and decrease of oxygen mobility due to hampering cooperative mechanism, however, this effect is less pronounced compared to A-site stoichiometric Nd nickelates which can be attributed to oxygen vacancies formation and their participation in cooperative migration as well as to other features of A-site deficiency. High mixed ionic-electronic conductivity of materials makes them promising in using as solid oxide fuel cells’ cathodes and oxygen separation membranes.