This study investigated the efficacy of using phosphate-modified zeolite (PZ) as an adsorbent for removing thorium from aqueous solutions. The effects of various factors such as contact time, adsorbent mass, initial thorium concentration, and pH value of the solution on the removal efficiency were analyzed using the batch technique to obtain optimum adsorption condition. The results revealed that the optimal conditions for thorium adsorption were a contact time of 24 h, 0.03 g of PZ adsorbent, pH 3, and a temperature of 25 °C. Isotherm and kinetics parameters of the thorium adsorption on PZ were also determined, with equilibrium studies showing that the experimental data followed the Langmuir isotherm model. The maximum adsorption capacity (Qo) for thorium was found to be 17.3 mg/g with the Langmuir isotherm coefficient of 0.09 L/mg. Using phosphate anions to modify natural zeolite increased its adsorption capacity. Furthermore, adsorption kinetics studies demonstrated that the adsorption of thorium onto PZ adsorbent fitted well with the pseudo-second-order model. The applicability of the PZ adsorbent in removing thorium from real radioactive waste was also investigated, and nearly complete thorium removal was achieved (> 99%) from the leached solution obtained from cracking and leaching processes of rare earth industrial residue under optimized conditions. This study elucidates the potential of PZ adsorbent for efficient removal of thorium from rare earth residue via adsorption, leading to a reduction in waste volume for ultimate disposition.