An assemblage of magnetite and apatite is common worldwide in different ore deposit types, including disparate members of the iron-oxide copper–gold (IOCG) clan. The Kiruna-type iron oxide-apatite deposits, a subtype of the IOCG family, are recognized as economic targets as well. A wide range of competing genetic models exists for magnetite–apatite deposits, including magmatic, magmatic-hydrothermal, hydrothermal(-metasomatic), and sedimentary(-exhalative). The sources and mechanisms of transport and deposition of Fe and P remain highly debatable. This study reports petrographic and geochemical features of the magnetite–apatite-rich vein assemblages in the dolerite dykes of the Gairdner Dyke Swarm (~0.82 Ga) that intruded the Roxby Downs Granite (~0.59 Ga), the host of the supergiant Olympic Dam IOCG deposit. These symmetrical, only few mm narrow veins are prevalent in such dykes and comprise besides usually colloform magnetite and prismatic apatite also further minerals (e.g., calcite, quartz). The genetic relationships between the veins and host dolerite are implied based on alteration in the immediate vicinity (~4 mm) of the veins. In particular, Ti-magnetite–ilmenite is partially to completely transformed to titanite and magmatic apatite disappears. We conclude that the mafic dykes were a local source of Fe and P re-concentrated in the magnetite–apatite veins. Uranium-Pb ages for vein apatite and titanite associated with the vein in this case study suggest that alteration of the dolerite and healing of the fractures occurred shortly after dyke emplacement. We propose that in this particular case the origin of the magnetite–apatite assemblage is clearly related to hydrothermal alteration of the host mafic magmatic rocks.