Rainbow trout (Oncorhynchus mykiss) confined to respirometer‐metabolism chambers were dosed with perfluorooctane sulfonate (PFOS) by intra‐arterial injection and sampled to obtain concentration time‐course data for plasma and either urine or expired water. The data were then analyzed using a 2‐compartment clearance‐volume model. Renal and branchial clearance rates (mL/d/kg) determined for all experiments averaged 19% and 81% of total clearance, respectively. Expressed as mean values for all experiments, the steady‐state volume of distribution was 277 mL/kg and the terminal half‐life was 86.8 d. Additional animals were exposed to PFOS in water, resulting in an average calculated branchial uptake efficiency of 0.36%. The renal clearance rate determined in the present study is approximately 75 times lower than that determined in earlier studies with perfluorooctanoate (PFOA). Previously, it was suggested that PFOA is a substrate for membrane transporters in the trout kidney. The present study suggests that glomerular filtration may be sufficient to explain the observed renal clearance rate for PFOS, although a role for membrane transporters cannot be ruled out. These findings demonstrate that models developed to predict the bioaccumulation of perfluoroalkyl acids by fish must account for differences in renal clearance of individual compounds. Environ Toxicol Chem 2016;35:717–727. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and as such, is in the public domain in the United States of America.