A critical challenge in modern chemical biology is the site-specific modification of proteins. This is due to the large number of reactive functional groups typically present in the cellular environment. An area of intense research is in developing methods for the site-specific modification of proteins, because it has a wide range of utility in fields such as chemistry, biology and medicine. Site-specific protein modification experiments have been useful for oriented protein immobilization, for studies of naturally-occurring post-translational modifications, for creating antibody-drug conjugates, for the introduction of fluorophores and other small molecules on to proteins, for examining protein structure, folding, dynamics and protein-protein interactions and for the preparation of protein-polymer conjugates. One the most important approaches toward protein labeling is to incorporate bioorthogonal functionalities into proteins at specific sites via enzymatic reactions. The incorporated tags would enable reactions that are chemoselective, whose functional groups are both inert in biological media, and which do not natively occur in proteins or other macromolecules. This review article summarizes the enzymatic strategies, which enables site-specifically functionalizing proteins with a variety of different functional groups. The enzymes covered in this review include formylglycine generating enzyme, sialyl transferase, phosphopantetheinyl transferase, O-GlcNAc post-translational modification, sortagging, transglutaminase, farnesyl transferase, biotin ligase, lipoic acid ligase and N-myristoyl transferase.