Simultaneous enantioseparation of three commonly used chiral antifungal pesticides (diniconazole, hexaconazole, and imazalil) was first studied based on micellar electrokinetic chromatography (MEKC) with hydroxypropyl-γ-CD (HP-γ-CD) as chiral selector. In this study, the importance of experimental parameters such as chiral selector type and concentration, sodium dodecyl sulfate (SDS) concentration, the ratio of methanol, and separation voltage in optimizing were investigated. The simultaneous enantioseparation of diniconazole, hexaconazole, and imazalil was successfully achieved in 30 mM borate buffer (pH 9.0) containing 10 mM HP-γ-CD and 20 mM SDS with methanol (8%) added as organic modifiers. The resolution of diniconazole, hexaconazole, and imazalil was 15.2, 2.12, and 2.78, respectively, and the peak efficiency (N) was over 566,825 plates/m. This study provides an alternative way to systematically separate chiral antifungal pesticides with high efficiency.