Restrictions on legacy per- and polyfluoroalkyl substances (PFASs) have led to the widespread use of emerging PFASs. However, their toxicokinetics have rarely been reported. Here, tissue-specific uptake and depuration kinetics of perfluoroethylcyclohexanesulfonate (PFECHS) and 6:2 and 8:2 chlorinated polyfluoroalkyl ether sulfonates (Cl-PFESAs) were studied in marine medaka (Oryzias melastigma). The fish were exposed to these substances for 28 days (0.2 μg/L), followed by a clearance period of 14 days. The depuration constant (kd) of PFECHS [0.103 ± 0.009 day–1 (mean ± standard deviation)] was reported for the first time. Among the six studied tissues, the highest concentrations of 6:2 Cl-PFESA, 8:2 Cl-PFESA, and PFECHS were found in the liver [1540, 1230, and 188 ng (g of wet weight)−1, respectively] on day 28 while the longest residence times were found in the eyes (t1/2 values of 21.7 ± 4.3, 23.9 ± 1.5, and 17.3 ± 0.8 days, respectively). No significant positive correlation was found between the bioconcentration factors of the studied PFASs and the phospholipid or protein contents in different tissues of the studied fish. Potential metabolites of Cl-PFESAs, i.e., their hydrogen-substituted analogues (H-PFESAs), were identified by time-of-flight mass spectrometry. However, the biotransformation rates were low (<0.19%), indicating the poor capacity of marine medaka to metabolize Cl-PFESAs to H-PFESAs.