Vanadium dioxide (VO2) manifests an abrupt metal–insulator transition (MIT) from monoclinic to rutile phases, with potential use for tunable electronic and optical properties and spiking neuromorphic devices. Understanding pathways to modulate electronic transport in VO2, as well as its response to irradiation (e.g., for space applications), is critical to better enable these applications. In this work, we investigate the selective modulation of electronic transport in VO2 films subject to different 10 keV helium ion (He+) fluences. Under these conditions, the resistivity in the individual monoclinic and rutile phases varied by 50%–200%, while the MIT transformation temperature remains constant within 4 °C independent of irradiation fluence. Importantly, different trends in the resistivity of the monoclinic and rutile phases were observed both as a function of total He fluence as well as in films grown on different substrates (amorphous SiO2/Si vs single crystal Al2O3). Through a combination of measurements including majority carrier sign via Seebeck, low frequency noise, and TEM, our investigation supports the presence of different kinds of point defects (V in; O in), which may arise due to grain boundary defect interactions. Our work suggests the utility of He irradiation for the selective modulation of VO2 transport properties for neuromorphic, in contrast to other established but non-selective methods, like doping.