Per‐ and polyfluoroalkyl substances are a class of fluorochemicals that can degrade into perfluoroalkyl acids, which are well known to be persistent in the environment. It is thus important that novel fluorinated surfactants be designed to degrade into small, nonbioaccumulative products. We report the biotransformation and elimination kinetics of one such novel polyfluorinated surfactant, di(polyfluoroether thioether(S)‐oate) sulfonate (diFESOS), and its metabolites. Biotransformation was investigated in vitro using S9 liver fractions and in vivo in Sprague–Dawley rats. Rats dosed by oral gavage with diFESOS were found to have relatively fast elimination kinetics, with half‐lives on the order of hours, compared with legacy fluorinated surfactants such as the disubstituted polyfluoroalkyl phosphates that have half‐lives on the order of days. To interrogate degradation of the polyfluorinated chain, rats were then dosed with a polyfluoroether thioether alcohol (a suspected product of carboxylate cleavage of diFESOS) either orally or intravenously, and the novel metabolite 2H‐3:2 polyfluoroether sulfonic acid (2H‐3:2 PFESA) was identified. Perfluoropropionic acid was detected in rat urine and is likely a terminal product. The blood of orally dosed rats contained higher levels of metabolites than the blood of intravenously dosed rats, suggesting the importance of metabolism in the gut and liver. Elimination kinetics of all the novel metabolites were faster than their fully fluorinated counterparts. Environ Toxicol Chem 2021;40:3328–3336. © 2021 SETAC