A simple and rapid TLC method using β-cyclodextrin as a chiral mobile phase additive (CMPA) was developed for direct separation of S-clopidogrel and its impurity R-clopidogrel. The influence of different factors (stationary phases, organic modifiers, chiral selectors and their concentrations in the mobile phase, and optimal saturation time of the chamber) on enantioseparation was studied. The best resolution of clopidogrel enantiomers was achieved on Polygram®cel 300 Ac-10% plates using isopropanol-0.5 mM β-cyclodextrin (6:4, υ/υ) as mobile phase in TLC chamber previously equilibrated with the mobile phase for 20 min. The spots were detected under UV light and using iodine vapours. The method enables rapid separation of clopidogrel enantiomers and can be successfully used in control of stereoselective synthesis of clopidogrel and in control of its purity. Finally, the molecular modelling of the inclusion complexes between the analytes and α-, β-, and γ-cyclodextrin was performed to investigate the mechanism of the enantiorecognition.