Fluorine is a very common element in the Earth’s crust and is present in the air, food, and in natural waters. It never meets in the free state in nature due to its high reactivity, and it comes in the form of fluorides. Depending on the concentration of fluorine absorbed, it may be beneficial or harmful to human health. Similar to any trace element, fluoride ion is beneficial for the human body at low levels, but as soon as its concentration becomes too high, it is toxic, inducing dental and bone fluorosis. The lowering of fluoride concentrations that exceed the recommended standards in drinking water is practiced in various ways around the world. The adsorption process has been classified as one of the most efficient methods for the removal of fluoride from water as it is environmentally friendly, easy to operate, and cost-effective. The present study deals with fluoride ion adsorption on modified zeolite. There are several influential parameters, such as zeolite particle size, stirring rate, solution pH, initial concentration of fluoride, contact time, and solution temperature. The maximum removal efficiency of the modified zeolite adsorbent was 94% at 5 mg/L fluoride initial concentration, pH 6.3, and 0.5 g modified zeolite mass. The adsorption rate increases accordingly with increases in the stirring rate and pH value and decreases when the initial fluoride concentration is increased. The evaluation was enhanced by the study of adsorption isotherms using the Langmuir and Freundlich models. The Langmuir isotherm corresponds with the experimental results of the fluoride ions adsorption with a correlation value of 0.994. The kinetic analysis results of the fluoride ions adsorption on modified zeolite allowed us to demonstrate that the process primarily follows a pseudo-second-order and then, in the next step, follows a pseudo-first-order model. Thermodynamic parameters were calculated, and the ΔG° value is found to be in the range of −0.266 kJ/mol up to 1.613 kJ/mol amidst an increase in temperature from 298.2 to 331.7 K. The negative values of the free enthalpy ΔG° mean that the adsorption of fluoride ions on the modified zeolite is spontaneous, and the positive value of the enthalpy ∆H° shows that the adsorption process is endothermic. The ∆S° values of entropy indicate the fluoride adsorption randomness characteristics at the zeolite-solution interface.