Fmoc-1-methyl-L-histidine is widely used in peptide synthesis, particularly in solid-phase peptide synthesis (SPPS) methods. Its primary application is as a protected amino acid derivative, where the Fmoc (fluorenylmethyloxycarbonyl) group serves as a temporary protecting group for the amino functionality during the synthesis process. This allows for the selective deprotection and coupling of amino acids in a controlled manner, enabling the construction of complex peptides with high precision.

The compound is especially valuable in the synthesis of histidine-containing peptides, where the methylation of the histidine side chain can influence the peptide's biological activity, stability, or interaction with other molecules. It is commonly employed in the production of peptides for research in biochemistry, pharmacology, and drug development, where modified histidine residues are required to study enzyme mechanisms, receptor-ligand interactions, or to develop therapeutic peptides. Additionally, its use extends to the preparation of peptide libraries for high-throughput screening in drug discovery.