A typical oil-in-water microemulsion (ME) was applied for the capillary electrophoretic separation of nonsteroidal anti-inflammatory drugs (NSAIDs). As the high-pH ME was introduced into the capillary and a voltage was applied, we observed an unusual phenomenon during the preconditioning process: a sharp inflection point occurred at 56.2 min (+/- 4.8%) (N = 15). Both before (region A) and after (region B) that point, a steady state was observed. Highly reproducible results were obtained for this event. Two different absorbance patterns were observed for the hydrostatic injection of either freshly prepared ME or ME collected from the outlet of the capillary column during the steady state of region B. The latter had an inflection point at approximately 9 min, whereas the former had a constant absorbance over the entire range. To further characterize this property, regions A and B were used for the separation of NSAIDs. The results showed that both the detection limit and the reproducibility of the separation were superior in region B. For deep insight into the stability of the ME in an electric field, the effects of the oil, cosurfactant, pH, and voltage were systematically investigated in the neat ME. From our findings, it can be concluded that the inflection time might be the migration time of the ME in an electric field, and it might actually be the result of equilibration. Moreover, the existence of many unexpected phenomena seems to be the result of a change in the properties of ME droplet in an electric field.