This paper quantitatively determines the occurrences of potentially toxic elements in Carboniferous kaolin in southwestern Sinai, Egypt. This research describes, in detail, the experimental treatment optimization to be used in pharmaceutical applications. The concentrations of As, Co, Ni, Pb, and V in these kaolin deposits exceed the Permitted Concentrations of Elemental Impurities for oral use in pharmaceutical applications. Herein, six desorbing agents (acetic acid, citric acid, DTPA, EDDS, EDTA, and NTA) were utilized as extracting solutions in batch-wise extractions to select the proper reagents. Parameters such as the pH, the mixing speed and time, and the solid–solution ratio were varied to optimize the extraction conditions. The findings indicate that citric acid and EDTA were effective in the removal of the aforementioned elements. The results reveal that the optimum removal of potentially toxic elements from kaolin can be achieved using citric acid and EDTA concentrations of 0.2 M and 0.1 M, respectively, for the treatment of 5 g of kaolin, under a pH of 4 for citric acid, and a pH of 10 for EDTA. The ideal mixing speed and time are 500 rpm and 6 h, respectively. Using 1:10 S/L of citric acid and EDTA showed removal rates of 100% for all the investigated PTEs. We recommend this treatment for different kinds of kaolin showing various degrees of contamination.