Special features of fluorination of thermoplastic polyurethane elastomers (TPE) are considered. A dependence of the fluorination level of TPE on the fluorination time and the atomic structure of the modified surface layer is detected. A significant effect of fluorination on the surface morphology of TPE, its physical and mechanical properties, flammability, and resistance to fuels and lubricants is determined and studied. The surface morphology of a fluorinated sample in comparison with a virgin one becomes more developed owing to the emergence of a high-frequency component. The formation of this structure is determined by a more intense fluorination of elastic, less dense polymer regions, to large depth and with partial destruction. A decrease in the swelling rate of the samples in aviation kerosene and motor oil is shown. It was found that surface fluorination reduces flammability of the thermoplastic elastomer with respect to such indicators as ignition time, burning-out height, and maximum flame height. In general, according to the Federal Aviation Regulations FAR-25, fluorination of thermoplastic elastomers shifts them from the category of “burning” into the category of “self-extinguishing.”