A novel, highly accurate sample injection system for capillary electrophoresis (CE) was developed based on an inkjet microchip capable of reproducing exact introduction volumes at the picoliter level. The difficulty in analyte discrimination using electrokinetic injection was also overcome using this injection method. The injection system consisted of an XY stage, an inkjet droplet ejection microchip, and a reservoir with a plug-in septum. To evaluate the precision of the system, a mixture of NBD-labeled amino acids consisting of Gly, L-Phe, L-Asp, and L-Ser was separated, and the performance was compared with that of traditional hydrodynamic and electrokinetic injection methods. The results demonstrated that the introduced volume highly relied on the number of droplets with low relative standard derivation (RSD) and good linear correction coefficient in the proposed injection method. In addition, a urine sample was analyzed via CE coupled with the inkjet injection system for the detection of the amino acid taurine. The concentration of urinary taurine was determined to be 2.42 ± 0.08 μM (confidence level, 95%; RSD, 1.05%; n = 4) with a recovery of 98.92-109.54% (n = 3). These results demonstrate the inkjet injection system we developed has the potential to revolutionize capillary electrophoretic separation in practical and commercial applications that require an automated accurate injection system.