Per- and polyfluoroalkyl substances (PFAS) are widely recognized as emerging contaminants because they are ubiquitous in various environmental media. Their potential for chronic toxicity after prolonged human exposure is a growing concern. Consequently, there is an urgent need to develop an appropriate technology to efficiently treat and rapidly and consistently monitor PFAS levels. This study reports the development of the first aptamers that can bind to perfluorooctanesulfonic acid (PFOS), with a dissociation constant (KD) of 6.76 μM, and exhibit a high specificity for PFOS even in the presence of other PFAS. The binding site and mechanism of the prepared aptamers are explored using truncation and molecular dynamics simulations, which show that the lengths of fluorocarbons and functional groups are important recognition epitopes. To demonstrate the application potential of the prepared aptamers, an aptamer-based quantitative polymerase chain reaction method is also developed, which exhibits picomolar-level detection capabilities and a limit of detection of 5.8 pM (2.9 ng/L), indicating its high sensitivity. Our findings demonstrate the potential of the developed method in the rapid in situ monitoring of PFOS at contamination sites, which will facilitate its early detection before rigorous analysis.