N,N'-Bis(benzyloxycarbonyl)guanidine is primarily used in organic synthesis as a protective group for guanidine functionalities. Its application is crucial in peptide chemistry, where it helps to protect guanidine groups during complex reactions, preventing unwanted side reactions. This compound is also employed in the synthesis of biologically active molecules, particularly in the development of pharmaceuticals and agrochemicals. Its stability under various reaction conditions makes it a valuable tool in multi-step synthetic processes, ensuring the integrity of the guanidine moiety until the final deprotection step. Additionally, it finds use in the preparation of intermediates for drug discovery, where precise control over functional groups is essential.