The elucidation of the oxygen ionic transport mechanism in atomic scale is important for finding the essential element of the higher efficiency and the wider oxygen content range in the application such as three-way catalysis or SOFC. In this study, the oxygen ionic transport properties of Sr3Fe2O7-δ are investigated as a function of its oxygen content by using density functional theory within the GGA+U methods. The calculated activation energy in Sr3Fe2O6.0 exhibits a higher migration barrier of 1.35 eV, while those in Sr3Fe2O6.25-6.75 are below 1.09 eV. To elucidate the difference of activation energy in Sr3Fe2O7-δ, we calculated the electronic and magnetic properties, which vary depending on the oxygen content and should affect the oxygen ionic transport. In our calculation, the energy band gap of 2.2 eV and the G-type antiferromagnetic ordering in Sr3Fe2O6.0 are well reproduced. The insulating phase in Sr3Fe2O6.25-6.5 is reproduced, and the magnetic phase transition from antiferromagnetic to incommensurate antiferromagnetic ordering within the planar FeO2 is also reasonably reproduced within our collinear calculation. In terms of the oxygen diffusion, we found that the vacancy at the O3 site between the bilayers of FeO6 is energetically the most stable and the vacancy at the apical O3 site moves more easily to an adjacent equatorial O1 site of FeO6 than in other directions for vacancy redistribution. The obtained activation energy of the O1 → O3 pathway is 1.09 eV, which agrees with the experimental value. The added O3 atom induces Jahn-Teller distortion, which is related not only with the insulating phase in Sr3Fe2O6.25-6.5 but also with the lower activation energy in Sr3Fe2O6.25-6.75, compared with Sr3Fe2O6.0.