Polycrystalline Sr1−xTi0.9Nb0.1O3−δ (x = 0, 0.1, 0.2) ceramics have been prepared by the solid state method and their structural and thermoelectric properties have been studied by neutron powder diffraction (NPD), thermal, and transport measurements. The structural analysis of Sr1-xTi0.9Nb0.1O3−δ (x = 0.1, 0.2) confirms the presence of a significant amount of oxygen vacancies, associated with the Sr-deficiency of the materials. The analysis of the anisotropic displacement parameters (ADPs) indicates a strong softening of the overall phonon modes for these samples, which is confirmed by the extremely low thermal conductivity value (κ ≈ 1.6 W m-1 K−1 at 823 K) found for Sr1−xTi0.9Nb0.1O3−δ (x = 0.1, 0.2). This approach of introducing A-site cation vacancies for decreasing the thermal conductivity seems more effective than the classical substitution of strontium by rare-earth elements in SrTiO3 and opens a new optimization scheme for the thermoelectric properties of oxides.