The intercalation of kaolinite through the insertion of ions or molecules amongst the structural aluminosilicate layers is a vital process in numerous clay-based applications and products. Layer neutrality and hydrogen bonding limits direct intercalation into kaolinite, other than for small molecules. Synthesizing zirconia-intercalated kaolinite is not a straightforward matter. To overcome this barrier, raw Egyptian kaolin (UnK) or its acid-activated product (HK) was sonicated and impregnated in aqueous ZrOCl2·8H2O solution followed by thermal treatment at various temperatures (100, 200, 300, and 500°C). The intercalation process was confirmed using various spectroscopic and analytical techniques. The direct intercalation of ZrO2 into the kaolinite layers was observed even through a mild thermal treatment (100, 200, and 300°C). The mechanism of intercalation was suggested to occur by binding ZrO2 to the Si/AlO groups with a preference for the acid-activated HK, causing variable enlargements of the basal spacing and producing very perturbed layers. Interestingly, the surface area increased by 250% as a result of zirconia intercalation. Scanning electron microscopy (SEM) images showed a remarkable improvement in the stacking order of the kaolinite particles. The impact of ZrO2 intercalation into kaolinite also enhanced its adsorption efficiency for Pb2+, Cu2+, and Cd2+ ions. Preliminary investigations showed that the zirconia-intercalated HK demonstrated a removal efficiency, which is three times greater than that of pristine HK. The adsorption tendency toward Pb2+ ions was greater than those of Cu2+ and Cd2+ and followed the order: Pb2+ >> Cu2+ > Cd2+. The study suggests that the chemical modification of kaolin by zirconia via a direct intercalation technique, which greatly improves its functionality as demonstrated by the selective sorption of heavy metal ions, is worthy of further study.