2-Amino-6-methylpyrimidine-4-thiol is primarily used in the synthesis of pharmaceuticals, particularly in the development of antiviral and antibacterial agents. Its structure allows it to act as a key intermediate in creating compounds that target specific enzymes or proteins in pathogens. Additionally, it finds application in organic chemistry research as a building block for more complex heterocyclic compounds. Its thiol group also makes it useful in coordination chemistry, where it can form stable complexes with metal ions, aiding in the study of metal-ligand interactions.