Soil electrokinetic remediation (SEKR) is a proven technique for treating inorganic, organic, and radionuclide pollutants, particularly in fine-grained soils. The main obstacle to implementing SEKR is the high pH zone adjacent to the cathode surface, which adversely affects electromigration and electroosmosis mechanisms. There have been many attempts to overcome this drawback, but most of the intended solutions are impractical due to excessive cost or the need for chemical additives. We developed a new process for soil electrokinetic treatment in which the cathode is a vertical perforated pipe inserted into the soil. The removals of Pb2+ and Zn2+ from kaolinite were evaluated using the Taguchi approach, in which the effects of five four-level parameters (operation time, electrical potential, cathode gap, concentration, and hydrostatic head) were analyzed. The perforated cathode pipe SEKR system (PCPSS) was designed to investigate vertical soil electrokinetic remediation, which has not been extensively studied. The obtained results showed that increasing the cathode gap and hydrostatic head enhanced electroosmosis role. Satisfactory removal of Zn2+ (93.9%) was achieved, however the maximum removed Pb2+ was 42.7%. The removed Pb2+ and Zn2+ above the cathode gap was much better than the cathode. The effects of cathode gap, concentration, and hydrostatic head did not exhibit any influence on current passing.