We have developed an easy-to-operate and effective method for performing the sequential online analysis of enzyme reactions based on capillary electrophoresis (CE). The system was constructed by passing two capillaries through a sample vial at a distance of 5 μm between the capillary ends. Direct online sample injection and sequential CE analysis were achieved by periodically switching the high-voltage power supply off and on, without any physical disturbance of the capillary inlet. The sample was injected via concentration diffusion with in-column derivatization of the amino acids occurring at the interface of the capillaries. High reproducibility of the sequential injections was demonstrated with relative standard deviation values (n = 20) of 1.01%, 1.25%, and 0.80% for peak height, peak area, and migration time, respectively. Sequential online CE enzyme assay of a glutamate pyruvate transaminase catalyzed enzyme reaction was carried out by simultaneously monitoring the substrate consumption and the product formation every 30 s from the beginning to the end of the reaction. The Michaelis constants for the reaction were obtained and were found to be in good agreement with the results of traditional off-line enzyme assays. Our method has great potential for usage in sequential online CE analysis of chemical reactions with in-column chemical derivatization of the analytes for ultraviolet or laser-induced fluorescence detection.