Preparative scale supercritical fluid chromatography was used for isolating and purifying uncommon non‐methylene interrupted or acetylenic polyunsaturated fatty acids ethyl esters from seed oils. Fractionation of Biota orientalis seed oil ethyl esters was performed by supercritical fluid chromatography to obtain juniperonic acid [(5Z,11Z,14Z,17Z)‐eicosa‐5,11,14,17‐tetraenoic acid], a non‐methylene interrupted polyunsaturated fatty acid. Fractionation of sandalwood seed oil ethyl esters yielded ximenynic acid [(E)‐octadec‐11‐en‐9‐ynoic acid], an acetylenic polyunsaturated fatty acid. The effects of CO2 flow rate, column stationary phase and particle size were explored to optimize ximenynic and juniperonic ethyl ester recovery and purity from ethyl ester mixtures using online UV/Vis detection. Particle size, followed by the stationary phase, were found to be the most important parameters to achieving good separation. Under optimized conditions, ximenynic and juniperonic ethyl ester purities greater than 99 and 95%, respectively, were achieved in a one step process without co‐solvent. The isolation and recovery of juniperonic acid from biota seed oil free fatty acids was also attempted. Using free fatty acids as the feed material, the non‐methylene interrupted polyunsaturated sciadonic acid was also able to be separated from other compounds including juniperonic acid under some conditions, and gave an increase in concentration of more than 17 times.