Defects in GaN can cause degradation in the active regions of GaN-based devices; however, the origin of such defects remains unclear. Here, the electron–phonon interaction around Ga vacancies (VGa) in GaN is investigated quantitatively using first-principles calculations. It is shown that the energy shift in an electronic system with a localized phonon mode has the same order of magnitude as that in an atomic system. Next, the phononic structures of a system in a positively charged state are calculated. It is demonstrated that localized modes in the neutral state are still localized under slightly shifted frequencies. These results indicate that a VGa satisfies all conditions for the phonon-kick mechanism. This characteristic is expected to result in enhancement of the amplitude of the localized modes, which should cause N atoms to migrate toward VGa sites and form a NGa–VN complex defect. Hence, the migration energies of N atoms from VGa sites to NGa–VN complex defects in both neutral and positively charged states are investigated. It is revealed that the migration barrier is smaller in the positively charged state than in the neutral state and that the NGa–VN complex is more stable than a VGa. In light of these findings, the conformation change from a VGa to a NGa–VN complex may serve as a microscopic mechanism for the first stage of the defect reactions around VGa sites in GaN. These findings are expected to be useful in the future development of light-emitting diodes and transistors with longer lifetimes and higher efficiencies.