A capillary electrophoresis method was developed and validated for the determination of the purity of dapoxetine with regard to the related substances (3S)-3-amino-3-phenylpropan-1-ol, (3S)-3-(dimethylamino)-3-phenylpropan-1-ol, 1-naphthol and the enantiomer (R)-dapoxetine. The separation was based on a dual selector system, which was optimized by a fractional factorial resolution V + design followed by a central composite face centered design with star distance 1 and Monte Carlo simulations for defining the design space. The optimized background electrolyte consisted of a 50 mM sodium phosphate buffer, pH 6.3, containing 45 mg/mL sulfated γ-cyclodextrin and 40.2 mg/mL 2,6-dimethyl-β-cyclodextrin. Separations were carried out in a 23.5/32 cm, 50 μm fused-silica capillary employing a separation voltage of 9 kV at 15 °C. Following robustness testing using a Plackett-Burman design the method was validated according to the International Council on Harmonization guideline Q2(R1) in the range of 0.05–1.0% relative to the dapoxetine concentration. The method was applied to the analysis of drug substance and a commercial tablet. Data regarding the enantiomeric purity of dapoxetine obtained by the capillary electrophoresis assay were comparable to the data obtained by an enantioselective HPLC method.