The rapid separation of a triacylglycerol positional isomer (TAG-PI) pair was examined via high-performance liquid chromatography-atmospheric pressure chemical ionization tandem mass spectrometry using an octacocyl silylation (C28) column. A TAG-PI pair binding two palmitic acids and one fatty acid that structurally differs from palmitic acid was separated at 10°C and 15°C using acetone as the mobile phase. However, the TAG-PI pair binding two unsaturated fatty acids and one saturated fatty acid was not separated by the C28 column. The results indicate that the structures of the two palmitic acids (saturated fatty acids) and the other fatty acid at the α or β position in TAG play an important role in the separation of the TAG-PI pair, and that the structure of the fatty acid needs to be considerably different from that of the palmitic acid, specifically in terms of the chain length or the location of the double bond.