The aim of this study was to establish an analytical method for the determination of E,E-farnesol and squalene in makgeolli, which is a traditional type of Korean fermented rice wine. E,E-farnesol and squalene in makgeolli were extracted using stir bar sorptive extraction (SBSE) coupled with gas chromatography-mass spectrometry. SBSE was found to be an effective method for analyzing the E,E-farnesol and squalene levels in makgeolli. The linear dynamic range of the SBSE method for detecting E,E-farnesol and squalene ranged from 0.5 to 200 ng/mL with $R^2=0.9974$ for E,E-farnesol and 100 to 50000 ng/mL with $R^2=0.9982$ for squalene. The limit of detection and the limit of quantification using the SBSE method were 0.1 and 0.5 ng/mL for E,E-farnesol and 15.0 and 40.0 ng/mL for squalene, respectively. The average recoveries obtained were, quantitatively, 101-107% for E,E-farnesol and 98-103% for squalene, respectively, supporting the accuracy of the SBSE-GCMS method.