Methyl 5-nitro-2-furoate is primarily used in organic synthesis as a key intermediate for the preparation of various pharmaceutical compounds. It is particularly valuable in the development of antimicrobial and antifungal agents due to the presence of the nitro group, which enhances biological activity. Additionally, it serves as a building block in the synthesis of heterocyclic compounds, which are crucial in medicinal chemistry for designing drugs with specific therapeutic effects. Its application extends to research laboratories where it is utilized in studies focusing on the development of novel bioactive molecules.