A reverse phase enantio-selective high performance liquid chromatographic method was developed for enantiomeric separation of 2-(1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purine-7(6H)-yl)-N’-(3-fluorobenzylidene)-propanehydrazide isomers. The enantiomers of 2-(1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purine-7(6H)-yl)-N’-(3-fluorobenzylidene)propanehydrazide were resolved on a ACE®Equivalence™ С18 (250 × 4.6 mm, 5 μm) column using a mobile phase system containing methanol, water, phosphate buffer рН 7.4 (50:46:4 v/v/v). The resolution between enantiomers was found to be more than 2.0. The sample solution and mobile phase were found to be stable for at least 48 h. The final optimised method was successfully applied to separate the (R)- and the (S)-enantiomers of 2-(1,3-dimethyl-2,6-dioxo-2,3-dihydro-1H-purine-7(6H)-yl)-N’-(3-fluorobenzylidene)-propanehydrazide and was proven to be reproducible and accurate.