Site-specific introduction of noncanonical amino acids (ncAAs) by genetic codon expansion enables manipulation of protein structure and function at the atomic level. More than 200 ncAAs have been incorporated into proteins by this method in different organisms, including plants and animals, and its application has been expanded to the development of new generation biotherapeutics. With the ability to introduce biorthogonal reactive groups into proteins site-specifically, genetic code expansion could not only improve the safety and efficacy of protein and peptide drugs, but also provide a pioneering solution for the prevention and treatment of human diseases. Here, we reviewed recent advances of genetic codon expansion and focused on its applications in protein and peptide drugs. Using genetic codon expansion, homogeneous antibody-drug conjugates with improved pharmacokinetic property could be constructed. Bispecific antibodies with flexible PEG-linkers constructed by ncAAs-based biorthogonal reaction could overcome the spatial arrangement limitation existed in the traditional methods, which generated the bispecific antibodies mainly relying on genetic fusion. Development of genetic codon expansion-based protein switch could improve the efficiency of cell therapy. Site-specifically modified cytokines with PEG and immobilized them on solid surface by genetic codon expansion could also improve their pharmacological properties. Incorporation of immunogenic ncAAs in proteins could elicit immune responses and be used to develop therapeutic protein vaccines. We believe that genetic code expansion could be widely used in the next generation protein and peptide drugs.