Capillary electrophoresis (CE) has become a useful analytical tool for the analysis of microdialysis samples. However, CE with UV detection (CE-UV) is not sensitive enough to quantify glutathione (GSH) and glutathione disulfide (GSSG) in high ionic strength sample matrices such as microdialysates, because of the small optical path length in the capillary. To overcome this limitation, an on-column preconcentration technique, pH-mediated base stacking, was used in this study to improve the sensitivity of CE-UV. In pH-mediated base stacking, sample injection is followed by the injection of sodium hydroxide to achieve on-column preconcentration of analytes. This stacking technique allowed large volumes of high ionic strength samples to be injected without deterioration of the separation efficiency and resolution. The limit of detection for GSH and GSSG was found to be 0.75 µM (S/N = 6) and 0.25 µM (S/N = 6), respectively. A 26-fold increase in sensitivity was achieved for both GSH and GSSG using the pH-mediated base stacking, relative to normal injection without stacking. The developed method was used to analyze GSH and GSSG in liver microdialysates of anesthetized Sprague Dawley male rats. The basal concentrations of GSH and GSSG in the liver microdialysates of male rats were found to be 4.73 ± 2.08 µM (n = 7) and 5.52 ± 3.66 µM (n = 7), respectively.