ABSTRACT GaV Se is one of the lacunar spinel materials able to host magnetic skyrmionic textures. Earlier investigations at temperatures below its Jahn–Teller ferroelectric phase transition disclosed a nanoscale ferroelectric domain separated by 109 domain walls. Here, we have investigated the impact of this nanoscale twinning on polar phonon modes. We report dielectric and reflectivity spectra of GaV Se crystal in the phonon frequency region, derived from the ab initio predicted phonon frequencies, eigenvectors and Born-effective charges. Reflectivity spectra of the nanotwinned crystal, calculated using exact expressions for the effective macroscopic dielectric response of a perfect regular twin, are compared with the predicted reflectivity spectra of single-domain crystal. A characteristic spectral feature caused by the nanoscale twinning has been identified. While this feature is not a well-defined geometric resonance, it may still be accessible in experiments.