A novel method was proposed for simultaneous determination of artesunate (ATS) and mefloquine (MFQ) in fixed-dose combination tablets by capillary zone electrophoresis with simultaneous direct and indirect detection by ultraviolet (CZE-UV). The background electrolyte, consisting of 30/15 mmol L-1 TRIS/3,5-dinitrobenzoic acid buffer at pH 8.2, a chromophore buffer, was selected taking into account a detailed study involving the effective mobility vs. pH curves of the analytes and electrolyte compounds in association with the very low molar absorptivity of ATS. Suitable separation conditions, considering voltage, temperature and buffer concentration as factors, were achieved through the 33 Box-Behnken design investigation. The optimum baseline separation conditions were: injection pressure of 30 mbar for 10 s, cartridge temperature of 22.5 °C and positive voltage of +30 kV. The method proved to be rapid (5 minutes), simple, selective, linear (r2 > 0.98), precise (relative standard deviation (RSD): ATS < 2.9% and MFQ < 2.2%) and accurate (recoveries: ATS 98.13-102.96% and MFQ 98.75-106.77%), proving to be suitable for routine quality control analysis.