The emergence of magnetic skyrmions, topological spin textures, has aroused tremendous interest in studying the rich physics related to their topology. While skyrmions promise high-density and energy-efficient magnetic memory devices for information technology, the manifestation of their non-trivial topology through single skyrmions, ordered, and disordered skyrmion lattices could also give rise to many fascinating physical phenomena, such as the chiral magnon and skyrmion glass states. Therefore, generating skyrmions at designated locations on a large scale, while controlling the skyrmion patterns, is key to advancing topological magnetism. Here, we present a new, yet general, approach to the ‘printing’ of skyrmions with zero-field stability in arbitrary patterns on a massive scale in exchange-biased magnetic multilayers. By exploiting the fact that the antiferromagnetic order can be reconfigured by local thermal excitations, we use a focused electron beam with a graphic pattern generator to ‘print’ skyrmions, which we refer to as skyrmion lithography. Our work provides a route to design arbitrary skyrmion patterns, thereby establishing the foundation for further exploration of topological magnetism.