(S)-2-Methylmorpholine hydrochloride is widely used as a chiral building block in the synthesis of various pharmaceutical compounds. Its stereochemistry makes it valuable in the production of enantiomerically pure drugs, particularly in the development of active pharmaceutical ingredients (APIs) for central nervous system disorders.

It serves as a key intermediate in the preparation of compounds like antipsychotics and antidepressants, where the specific stereochemistry is crucial for biological activity. Additionally, it is employed in organic synthesis as a reagent or catalyst in asymmetric reactions, aiding in the creation of complex molecules with high enantiomeric purity.

In the agrochemical industry, it is utilized in the synthesis of chiral pesticides and herbicides, ensuring targeted action and reduced environmental impact. Its versatility in chemical reactions and role in producing optically active compounds make it a significant component in both pharmaceutical and agrochemical research and manufacturing.