Self-organized silicide nanowires are considered as main building blocks of future nanoelectronics and have been intensively investigated. In nanostructures, the lattice vibrational waves (phonons) deviate drastically from those in bulk crystals, which gives rise to anomalies in thermodynamic, elastic, electronic, and magnetic properties. Hence, a thorough understanding of the physical properties of these materials requires a comprehensive investigation of the lattice dynamics as a function of the nanowire size. We performed a systematic lattice dynamics study of endotaxial FeSi2 nanowires, forming the metastable, surface-stabilized α-phase, which are in-plane embedded into the Si(110) surface. The average widths of the nanowires ranged from 24 to 3 nm, their lengths ranged from several µm to about 100 nm. The Fe-partial phonon density of states, obtained by nuclear inelastic scattering, exhibits a broadening of the spectral features with decreasing nanowire width. The experimental data obtained along and across the nanowires unveiled a pronounced vibrational anisotropy that originates from the specific orientation of the tetragonal α-FeSi2 unit cell on the Si(110) surface. The results from first-principles calculations are fully consistent with the experimental data and allow for a comprehensive understanding of the lattice dynamics of endotaxial silicide nanowires.