We report the effects of oxygen deficiency to the electronic and magnetic properties of SrCoO3 calculated using spin-polarized Density Functional Theory. The correlation effects of the Co 3d orbitals are considered explicitly using the effective Hubbard U eff parameter. The U eff consists of the subtraction between the U value of 3 eV to denote the Coulomb interaction and the Hund’s coupling parameter J of 0.95 eV. Our results show that the localized character of the Co 3d orbitals strongly depends on the oxygen content. The magnetic exchange interaction between two neighboring Co ions is therefore altered. As a consequence, a change of magnetic ground state using the same U eff value from ferromagnetic ordering in full oxygen content to antiferromagnetic ordering in SrCoO2.5 is obtained.