Methyl 5,6-diaminonicotinate is primarily used as an intermediate in the synthesis of various pharmaceutical compounds. It plays a crucial role in the development of drugs targeting neurological disorders, particularly those involving nicotinic acetylcholine receptors. This compound is also utilized in the production of agrochemicals, where it contributes to the creation of pesticides and herbicides. Additionally, it serves as a building block in organic chemistry research for the synthesis of complex molecules with potential therapeutic applications. Its versatility makes it valuable in both industrial and academic settings for advancing drug discovery and chemical innovation.