Determination of free fatty acids (FFAs) in food products is of enormous interest mainly because they are related to the quality and authenticity of the oils. In this study, supercritical fluid chromatography (SFC), followed by an electrospray ionisation triple–quadrupole mass spectrometry (ESI-MS), is shown to provide a novel method for the separation and detection of FFAs in edible oils without any pretreatment. Eight FFAs were separated on a HSS C18 SB column with gradient elution within 3min. Effects of different columns, modifiers and column temperature changes were evaluated. The results indicated the feasibility of this method for the high-throughput determination of individual FFAs with satisfactory correlation coefficients (R2>0.994) and good reproducibility of RSD<13.5% (intraday) and <15.0% (interday). By combined with principal component analysis (PCA), different types of edible oil were successfully distinguished into several categories, showing a potential application for the determination of oil quality or authenticity.