Protein, nucleic acid, and small-molecule drugs frequently require chemical modification with polymers such as polyethylene glycol (PEG), to increase their in vivo circulation time and reduce their immunogenicity. Previously, we developed low-immunogenic zwitterionic polycarboxybetaine (PCB) to replace PEGylation. Herein, we delineate the design principles of zwitterionic polypeptide to mimic PCB. These studies establish an EKP polypeptide composed of glutamic acid (E), lysine (K), and proline (P) as a low-immunogenic, unstructured, zwitterionic peptide. Then, we demonstrate EKP peptide as a genetically encodable fusion protein platform. The unique zwitterionic design ensures high hydration, thereby increasing hydrodynamic size and improving stability. EKP fusion proteins achieve prolonged circulation, low immunogenicity, and maintained circulation time over multiple injections, thus avoiding accelerating blood clearance (ABC). Its performance substantiates EKP as a valuable platform technology for drugs and biologics. Display omitted •A low-immunogenic zwitterionic EKP peptide is identified and confirmed in vivo.•Therapeutic proteins fused with genetically encoded EKP improve their biophysical properties and in vivo performance.•EKP is established as a platform technology for drugs and biologics.