Helium atom scattering and density-functional theory (DFT) are used to characterize the phonon band structure of the (3 × 1)-O surface reconstruction of Nb(100). Innovative DFT calculations comparing surface phonons of bare Nb(100) to those of the oxide surface show increased resonances for the oxide, especially at higher energies. Calculated dispersion curves align well with experimental results and yield atomic displacements to characterize polarizations. Inelastic helium time-of-flight measurements show phonons with mixed longitudinal and shear-vertical displacements along both the 100, ΓX and 110, ΓM symmetry axes over the entire first surface Brillouin zone. Force constants calculated for bulk Nb, Nb(100), and the (3 × 1)-O Nb(100) reconstruction indicate much stronger responses from the oxide surface, particularly for the top few layers of niobium and oxygen atoms. Many of the strengthened bonds at the surface create the characteristic ladder structure, which passivates and stabilizes the surface. These results represent, to our knowledge, the first phonon dispersion data for the oxide surface and the first ab initio calculation of the oxide's surface phonons. This study supplies critical information for the further development of advanced materials for superconducting radiofrequency cavities. © 2022 Author(s).