Experimental investigations were carried out using kaolinite to adsorb two rare earth ions, lanthanum ion (La3+) and yttrium ion (Y3+), which will provide some useful information and new insights on the mineralization process and fractionation phenomenon of weathered crust elution-deposited rare earth ores. The results showed that the equilibrium adsorption capacity of Y3+ is greater than La3+ under the same experimental conditions. The adsorption of rare earth ions presents strongly temperature dependent indicating an endothermic adsorption process. The pseudo-first-order kinetic model and the pseudo-second-order kinetic model were applied to discuss the adsorption kinetics. It was found that the adsorption rate of rare earth follows the pseudo-second-order kinetic model among the adsorption temperature range. Furthermore, the adsorption process of rare earth ions on kaolinite followed the Langmuir isotherm model confirmed by the correlation of experimental equilibrium data to standard isotherm model, Langmuir and Freundlich isotherms. The activation energies for the adsorption of La3+ and Y3+ on kaolinite are 28.1903 kJ/mol and 25.4190 kJ/mol, respectively. All kaolinite before and after adsorption were characterized by XRD and SEM-EDX to understand the adsorption mechanism. The obtained results suggested that the adsorption of La3+ and Y3+ on kaolinite is an endothermic and chemisorption process.