Benzo[e]isatin is primarily used in organic synthesis as a key intermediate for the preparation of heterocyclic compounds. It serves as a building block in the development of biologically active molecules, including potential pharmaceuticals with antimicrobial, antiviral, and anticancer properties. Its structure allows for functionalization at multiple sites, making it valuable in medicinal chemistry research for designing novel drug candidates. Additionally, it is employed in the synthesis of dyes and fluorescent probes due to its extended aromatic system, which can enhance photophysical properties useful in imaging and sensing applications.