Since the advent of graphene ushered the era of 2D materials, many forms of hydrogenated graphene have been reported, exhibiting diverse properties ranging from a tunable bandgap to ferromagnetic ordering. Patterned hydrogenated graphene with micron‐scale patterns has been fabricated by lithographic means. Here, successful millimeter‐scale synthesis of an intrinsically honeycomb‐patterned form of hydrogenated graphene on Ru(0001) by epitaxial growth followed by hydrogenation is reported. Combining scanning tunneling microscopy observations with density‐functional‐theory (DFT) calculations, it is revealed that an atomic‐hydrogen layer intercalates between graphene and Ru(0001). The result is a hydrogen honeycomb structure that serves as a template for the final hydrogenation, which converts the graphene into graphane only over the template, yielding honeycomb‐patterned hydrogenated graphene (HPHG). In effect, HPHG is a form of patterned graphane. DFT calculations find that the unhydrogenated graphene regions embedded in the patterned graphane exhibit spin‐polarized edge states. This type of growth mechanism provides a new pathway for the fabrication of intrinsically patterned graphene‐based materials.