With its exceptional charge mobility, graphene holds great promise for applications in next-generation electronics. In an effort to tailor its properties and interfacial characteristics, the chemical functionalization of graphene is being actively pursued. The oxidation of graphene via the Hummers method is most widely used in current studies, although the chemical inhomogeneity and irreversibility of the resulting graphene oxide compromises its use in high-performance devices. Here, we present an alternative approach for oxidizing epitaxial graphene using atomic oxygen in ultrahigh vacuum. Atomic-resolution characterization with scanning tunnelling microscopy is quantitatively compared to density functional theory, showing that ultrahigh-vacuum oxidization results in uniform epoxy functionalization. Furthermore, this oxidation is shown to be fully reversible at temperatures as low as 260 °C using scanning tunnelling microscopy and spectroscopic techniques. In this manner, ultrahigh-vacuum oxidation overcomes the limitations of Hummers-method graphene oxide, thus creating new opportunities for the study and application of chemically functionalized graphene.