Perfluoroalkyl carboxylic acids (PFCAs) are a significant group of per- and polyfluoroalkyl substances (PFASs). They are persistent organic chemicals manufactured for their resistance to heat, water, and stains. PFCAs are ubiquitous in the environment, particularly in surface water and wastewater, because they are widely used in everyday consumer products. This contamination poses a risk to drinking water supplies and human health, necessitating sensitive and effective analytical methods. Traditional liquid chromatography–tandem mass spectrometry (LC-MS/MS) is commonly used but involves complex sample handling and high costs. In this study, we developed an enhanced stir bar sorptive extraction (SBSE) method coupled with thermal desorption–gas chromatography–mass spectrometry (TD-GC-MS) for the analysis of PFCAs in water. This method demonstrates linearity, with R2 values from 0.9892 to 0.9988, and low limits of detection (LOD) between 21.17 ng/L and 73.96 ng/L. Recovery rates varied from 47 to 97%, suggesting efficient extraction. Compared to traditional methods, the developed SBSE technique requires only a 1 mL sample volume and minimal amounts of solvents, enhancing eco-friendliness and reducing potential contamination and handling errors. This method also demonstrated good precision and robustness across various water matrices. Overall, the developed method offers a precise, eco-friendly, and reliable approach for analyzing PFCAs in diverse water samples.