A protocol for separation of positionally isomeric trans- and cis-octadecenoic fatty acids as their p-methoxyphenacyl esters, using a single column silver ion high-performance liquid chromatography (Ag-HPLC) with UV detection, is described. The procedure involves hydrolysis of oil to free fatty acids, derivatization to p-methoxyphenacyl esters, purification and separation by Ag-HPLC. The procedure is robust and relatively rapid. In total, it takes about 16 h or overnight and a further 5 h to carry out. Its feature and value consist in the application of p-methoxyphenacyl esters in Ag-HPLC, thus ensuring excellent simultaneous separation of both configurational and positional fatty acid isomers on a single column by a single run. Quantification is not affected by the fatty acid structure, and the method is highly sensitive. As fatty acid isomerization is a strong evidence for adulteration of lipid-containing food products with chemically modified oils and fats, the procedure is especially appropriate for detection and authenticity analysis in many areas of food manufacturing and quality control.