Silicon dangling bonds (DBs) on an adsorbate-covered Si(100) surface can be created in a scanning tunneling microscope (STM) with high precision required for a number of applications. However, vacancies containing DBs can diffuse, disrupting precisely created structures. In this work, we study the diffusion of Br vacancies on a Si(100)-2 × 1-Br surface in an STM under typical imaging conditions. In agreement with previous work, Br vacancies diffuse at a positive sample bias voltage. Here, we demonstrated that only vacancies containing a positively charged DB hop across the two atoms of a single Si dimer, while vacancies containing neutral and negatively charged DBs do not. Calculations based on density functional theory confirmed that positively charged Br (and Cl) vacancies have a minimum activation barrier. We propose that diffusion operates by both one-electron and two-electron mechanisms depending on the applied voltage. Our results show that the DB charge has a critical effect on the vacancy diffusion. This effect should be taken into account when imaging surface structures with charged DBs as well as when studying the diffusion of other atoms and molecules on the Si(100) surface with vacancies in an adsorbate layer.