A detailed study of the role of oxygen vacancies in determining the effective mass and high temperature (300–1000 K) thermoelectric properties of La-doped epitaxial SrTiO3 thin films is presented. It is observed that at intermediate temperatures, a transition from degenerate to non-degenerate behavior is observed in the Seebeck coefficient, but not electrical conductivity, which is attributed to heterogeneous oxygen non-stoichiometry. Heikes formula is found to be invalid for the films with oxygen vacancies. By fitting the spectroscopic ellipsometry (SE) data, obtained in the range 300–2100 nm, using a Drude-Lorentz dispersion relation with two Lorentz oscillators, the electrical and optical properties of the films are extracted. Using the excellent agreement between the transport properties extracted from SE modeling and direct electrical measurements, we demonstrate that an increase in concentration of oxygen vacancies results in a simultaneous increase of both carrier concentration and electron effective mass, resulting in a higher power factor.