Methyl 5-amino-6-chloronicotinate is primarily used as an intermediate in the synthesis of various pharmaceutical compounds. Its structure makes it a valuable building block for creating active pharmaceutical ingredients (APIs), particularly in the development of drugs targeting central nervous system disorders. It is also employed in the production of agrochemicals, where it serves as a precursor for creating pesticides and herbicides. Additionally, this compound finds use in organic synthesis for constructing complex molecules due to its reactive amino and chloro functional groups, which facilitate further chemical modifications. Its applications are largely focused on research and industrial-scale chemical manufacturing.