Ruminant milk is the lead source of conjugated linoleic acid (CLA) in the human diet, with cis-9, trans-11 CLA being the major among all. Small amounts of trans-10, cis-12 CLA are also found in synthetic supplements. Since both isomers are biologically active with potential health benefits, there is great interest in quantifying them for quality control routines. An alternative method for the analysis of the aforementioned CLAs by fast gas chromatography (GC) is discussed in the present study. The fatty acid methyl ester mixture obtained by alkaline catalysis was injected into a GC equipped with a fame ionization detector (FID) and fitted with an ionic liquid SLB-IL111 chromatographic column (15 m × 0.10 mm × 0.08 µm). Separation was achieved in less than 5 min using a 168 °C isotherm run. Both CLA isomers were quantified by using of single point standard addition statistical approach. Results were contested to those obtained using the recommended 100 m long CP-Sil88 capillary column and none evidence of significant differences was found within 95% confidence interval. Therefore, the proposed method could be valuable to focused regulatory routines of large numbers of samples with greater analytical frequency.