N-Benzylguanidinium acetate is primarily utilized in organic synthesis and pharmaceutical research. It serves as a key intermediate in the preparation of various biologically active compounds, particularly those targeting enzyme inhibition or receptor modulation. Its guanidinium moiety is often employed in the development of molecules with enhanced binding affinity to specific biological targets, making it valuable in drug discovery. Additionally, it is used in the synthesis of peptidomimetics and other small molecules that mimic peptide structures, aiding in the study of protein interactions and signaling pathways. Its application extends to materials science, where it is incorporated into the design of functionalized polymers and supramolecular assemblies.