2-Chloro-6-fluoroquinoxaline is primarily used in the field of organic synthesis and pharmaceutical research. It serves as a key intermediate in the development of various biologically active compounds, particularly in the synthesis of quinoxaline derivatives. These derivatives are often explored for their potential antimicrobial, anticancer, and antiviral properties. Additionally, this compound is utilized in the preparation of agrochemicals, contributing to the development of pesticides and herbicides. Its unique structure allows for further functionalization, making it valuable in the design of novel molecules for therapeutic and agricultural applications.