Using a hybrid density functional theory method combined with linear combination of atomic orbitals basis set and periodic supercell approach, the atomic, electronic structure, and phonon properties were calculated for SrTiO3 containing either Fe4+ substituting host Ti4+ ions or neutral oxygen vacancies Vo. For both defects, the Jahn–Teller effect occurs, thus reducing the cubic symmetry of a perfect crystal and leading to the appearance of both Raman- and infrared-active vibrational modes. The calculated phonon densities of states and group-theoretical analysis of defect-induced phonon frequencies were used for the interpretation of the relevant experimental data, once defect-induced local modes are identified. The temperature dependence of the Vo formation energy based on the calculated Gibbs free energy was also compared with experiments, and the phonon contribution therein estimated.