Pure form, single phase, and highly crystalline low-silica zeolite Y was synthesized from natural nanotubular halloysite mineral by the hydrothermal method. In the synthesis process, the halloysite consisted of SiO2 and Al2O3 was used as starting material with adding supplementary silica and alumina sources. Ammonium adsorption properties of the as-synthesized zeolite Y were studied using batch experiments and the results revealed that its adsorption properties were strongly dependent on contact time, adsorbent dosage, pH, ionic strength, temperature, and initial concentration. The equilibrium data fit well with the Langmuir isotherm compared with the Freundlich isotherm. Kinetic studies showed that the adsorption followed the pseudo-second-order model. Thermodynamic parameters such as change in free energy (G0), enthalpy (H0), and entropy (S0) were also determined, which indicated that the adsorption of ammonium on zeolite Y was a spontaneous and exothermic process at ambient conditions. Due to its low cost, high adsorption capacity and fast adsorption rate, the zeolite Y synthesized from halloysite has the potential to be utilized for the cost-effective removal of ammonium from wastewater.