Graphene (Gr) has been demonstrated to protect metallic thin films against oxidation. Based on this idea, we propose a new method to fabricate microstructured magnetic domains using patterned single-layer Gr. In the first experiment, single-layer Gr was transferred onto a CoPd alloy film pregrown on a SiO2/Si(001) substrate. Subsequently, the single-layer Gr was patterned through electron beam lithography followed by oxygen plasma etching to expose selective micron-sized areas of CoPd. The exposed areas of CoPd were more easily oxidized compared to the areas protected by Gr, which is found to result in significant magnetic contrast between the protected and surface-oxidized areas of CoPd. In the second experiment, a lithographically-patterned Gr layer was placed between the Fe and CoPd layers to block interlayer diffusion area-selectively during sample annealing. Magnetic contrast is observed to be established between the Pd/Fe/Gr/CoPd and Pd/Fe/CoPd areas, leading to a magnetic structure that matches the pattern of the lithographed Gr. These observations demonstrate that Gr patterning is a simple and powerful method for magnetic patterning, which can be applied in the fabrication of future data-storage and spintronic devices.