Trifluorothymine is primarily used in pharmaceutical research and development, particularly in the synthesis of antiviral and anticancer agents. Its modified structure enhances metabolic stability and binding affinity to target enzymes, making it valuable in nucleoside analog design. It serves as a key intermediate in creating fluorinated pyrimidine derivatives that interfere with DNA replication in rapidly dividing cells. This property is exploited in oncology for potential tumor growth inhibition. Additionally, due to its resistance to degradation by cellular enzymes, it improves the half-life of therapeutic compounds in vivo. Trifluorothymine is also utilized in biochemical studies to probe enzyme mechanisms involving thymidine metabolism.