The integration of two‐photon lithography (TPL) with magnetic material processing has opened transformative avenues for designing and realizing 3D functional nanomagnetic systems. This review presents a comprehensive overview of how TPL can be leveraged to fabricate 3D architectures that harness magnetism. The fundamental physics of TPL is examined, and recent advances in voxel engineering, resolution, and throughput are reviewed. Emerging strategies for magnetic functionalization, including physical vapor deposition, electrodeposition, conformal coating, and direct writing of magnetic nanostructures and composites, are thoroughly examined in the context of the functional material systems they enable. Applications in 3D nanomagnetism, such as artificial spin ices for neuromorphics, magnetic racetracks, and magnetic microrobots, are highlighted to demonstrate the versatility of TPL‐based fabrication platforms. Finally, a forward‐looking perspective is provided, which provides future research directions and associated challenges, including the integration of antiferromagnets, spin‐caloritronic materials, and altermagnets, as well as the development of neuromorphic magnetic architectures. In doing so, TPL is positioned as an essential method in the development of technologies based upon next‐generation 3D functional magnetic materials.