A new CE method using sulfobutylether-beta-cyclodextrin (SBE-beta-CD) as chiral additive was developed and validated for the determination of pantoprazole enantiomers. The primary factors affecting its separation efficiency, which include chiral selector, buffer pH, organic additive, and applied voltage, were optimized. The best results were obtained using a buffer consisting of 50 mM borax-150 mM phosphate adjusted to pH 6.5, 20 mg/mL SBE-beta-CD, and a 10 kV applied voltage. The optimized method was validated for linearity, precision, accuracy, and proved to be robust. The LOD and LOQ for R-(+)-pantoprazole were 0.9 and 2.5 mu g/mL, respectively. The method is capable of determining a minimum limit of 0.1% (w/w) of R-enantiomer in S-()-pantoprazole bulk samples.