A method using liquid chromatography-tandem mass spectrometry (LC-MS/MS) with QuEChERS (quick, easy, cheap, effective, rugged, and safe) sample preparation was developed for the simultaneous determination of 12 perfluorocarboxylic acids (PFCAs) and 7 perfluorosulfonic acids (PFSAs) in the muscle of shrimp, shellfish, and fish. A modified QuEChERS procedure was applied to the extraction and concentration of perfluorinated compounds (PFCs) as well as for removal of interferences. The determination of the 19 PFCs was performed by LC-MS/MS in negative-ion detection mode. 13C-labeled PFCs, as a stable isotopic internal standard (except for L-PFBS, L-PFPeS, ipPFNS, and L-PFNS, for which no labeled analogs were available), was used for calibration. The limits of detection ranged from 0.01–1.0 μg/kg. The recoveries of spiked sample at 0.02–8.0 μg/kg ranged from 61 to 117% with relative standard deviations of less than 14%. The developed method was successfully utilized to monitor real samples, which demonstrated that it is a simple, fast, and robust method and could be used to monitor PFCAs and PFSAs in aquatic products. Most of the samples tested positive, mainly for perfluorooctane sulfonate acid (PFOS), perfluorooctanoic acid (PFOA), and perfluorobutanoic acid (PFBA), but other samples of the 14 studied PFCs were also present.