Electrokinetic supercharging (EKS) is defined as a technique that combines electrokinetic sample injection with transient ITP. Quantitative repeatability of EKS-CZE and the other CE methods using electrokinetic sample injection process is usually inferior in comparison with the CE methods using hydrodynamic or hydrostatic injection. This is due to some effects, such as the temperature change and the convection of the sample solution in the reservoir, as well as the change of the distance between an electrode and a capillary end (D-ec). In particular, we have found that the D-ec change might most seriously affect the repeatability, especially when the electrode is a thin Pt wire that could be unintentionally bent during sampling. By using a Teflon spacer to fix D-ec to 1.1 mm, the RSD of peak area (n = 5) was decreased from 20 to 3.4% in EKS-CZE for several metal cations. This D-ec dependence of the sample amount injected was supported by computer simulation using CFD-ACE+ software. The improved repeatability (down to 5.1% at n = 5, averaged RSD for Co2+, Li+, Ni2+, Zn2+ and Pb2+) was also experimentally attained by increasing the D-ec to ca. 20 mm, which was also effective to obtain high sensitivity. Since the temperature and the convection effects on the repeatability are comparatively small in a proper laboratory environment, these effects were estimated from the EKS-CZE experiments using conditions such as warming and agitating the sample solution during EKS process. Finally, EKS-CZE was applied to the detection of ions from atmospheric electrolytes in high-purity water exposed to ambient air for 2 h. The microgram per liter levels of anions (chloride, sulfate, nitrate, formate, acetate and lactate) and cations (ammonium, calcium, sodium and magnesium) could be detected using conventional UV detector.