Abstract Protein assemblies have drawn much attention as platforms for biomedical applications, including gene/drug delivery and vaccine, due to biocompatibility and functional diversity. Here, the construction and functionalization of a protein assembly composed of human clathrin heavy chain and light chain for a targeted protein delivery, is presented. The clathrin heavy and light chains are redesigned and associated with each other, and the resulting triskelion unit further self‐assembled into a clathrin assembly with the size of about 28 nm in diameter. The clathrin assembly is dual‐functionalized with a protein cargo and a targeting moiety using two different orthogonal protein–ligand pairs through one‐pot reaction. The functionalized clathrin assembly exhibits about a 900‐fold decreased K D value for a cell‐surface target due to avidity compared to a native targeting moiety. The utility of the clathrin assembly is demonstrated by an efficient delivery of a protein cargo into tumor cells in a target‐specific manner, resulting in a strong cytotoxic effect. The present approach can be used in the creation of protein assemblies with multimodality.