Trans-2,6-dimethylmorpholine is primarily used as an intermediate in the synthesis of various pharmaceuticals and agrochemicals. Its structure allows it to act as a building block in the creation of more complex molecules, particularly those with morpholine rings, which are common in drug design. It is often employed in the development of antifungal agents, where its morpholine core contributes to the inhibition of ergosterol biosynthesis in fungi. Additionally, it finds utility in the production of herbicides and pesticides, where its chemical properties enhance the efficacy of these agricultural products. The compound is also explored in organic synthesis for the preparation of chiral ligands and catalysts, aiding in asymmetric synthesis processes.