AbstractOxygen vacancies, especially their distribution, are directly coupled to the electromagnetic properties of oxides and related emergent functionalities that have implications for device applications. Here using a homoepitaxial strontium titanate thin film, we demonstrate a controlled manipulation of the oxygen vacancy distribution using the mechanical force from a scanning probe microscope tip. By combining Kelvin probe force microscopy imaging and phase-field simulations, we show that oxygen vacancies can move under a stress-gradient-induced depolarisation field. When tailored, this nanoscale flexoelectric effect enables a controlled spatial modulation. In motion, the scanning probe tip thereby deterministically reconfigures the spatial distribution of vacancies. The ability to locally manipulate oxygen vacancies on-demand provides a tool for the exploration of mesoscale quantum phenomena and engineering multifunctional oxide devices.