The internal standard capillary electrophoresis method (IS-CE) has been implemented in a novel sequential injection–capillary electrophoresis instrument for the high-throughput determination of acidity constants (pKa) regardless of aqueous solubility, number of pKa values, or structure. This instrument comprises a buffer creation system that automatically mixes within a few seconds four reagents for in situ creation of the separation electrolyte with a pH range of 2–13, ionic strength of 10–100 mM and organic solvent content from 0% to 40%. Combined with 1.2 kV/cm and a short effective length (15 cm to the UV detector) fast 20 s electrophoretic separations can be obtained. The low standard deviation of the replicates and the low variation compared to reference values show that this system can accurately determine acidity constants of drugs by IS-CE. A single pKa can be determined in 2 min and a set of 20 measurements in half an hour, allowing rapid, simple, and flexible determination of pKa values of pharmaceutical targets.