Ethyl 5-amino-3-methoxypicolinate is primarily used in the synthesis of various pharmaceutical compounds. It serves as a key intermediate in the development of drugs targeting neurological disorders, particularly those involving the central nervous system. Its structure allows for modifications that enhance the efficacy of therapeutic agents, making it valuable in medicinal chemistry. Additionally, it is employed in the production of agrochemicals, where it contributes to the creation of pesticides and herbicides with improved activity and selectivity. Its role in organic synthesis also extends to the preparation of complex molecules for research and industrial applications.