The enantiomeric separation of antifungal compounds is an arduous task in pharmaceutical and biomedical fields due to the different properties that each diastereoisomer presents. The enantioseparation of a group of fungicides (sulconazole, bifonazole, triadimefon and triadimenol) using supercritical fluid chromatography was achieved in this work. For this goal, four different chiral columns based on polysaccharide derivatives, as well as the effect of different chromatographic parameters such as temperature, type and percentage of organic modifier (methanol, ethanol and isopropanol), were thoroughly investigated. The inversion of the elution order of enantiomers as a result of a change in the stationary phase or organic modifier was also evaluated by employing a circular dichroism detector. The best separation conditions, in terms of the enantioresolution and analysis time, were obtained with the Lux® Cellulose-2 column using isopropanol as the organic modifier.