Clean water is a precious and limited resource that plays a crucial role in supporting life on our planet. However, the industrial sector, especially the pharmaceutical industry, significantly contributes to water consumption, and this can lead to water body pollution. Fenton’s reagent was introduced in the current investigation to oxidize acetaminophen as an emerging pollutant in such effluents. Therefore, we employed a straightforward co-precipitation method to fabricate chitosan-coated magnetic iron oxide, which is referred to in this study as Chit@Fe3O4. X-ray diffraction spectroscopy (XRD), Fourier transform infrared (FTIR), diffuse reflectance spectra (DRS), scanning electron microscopy (TEM), and transmission electron microscopy (TEM) were utilized to characterize the sample. It is crucial to treat such effluents due to the rapid increase in emerging pollutants. In this study, a photo-Fenton system was introduced as a combination of a Chit@Fe3O4 catalyst augmented with hydrogen peroxide under ultraviolet (UV) illumination conditions. The results reveal that only 1 h of irradiance time is efficient in oxidizing acetaminophen molecules. Doses of 20 and 200 mg/L of Chit@Fe3O4 and H2O2, respectively, and a pH of 2.0 were recorded as the optimal operational conditions that correspondingly oxidize 20 mg/L of acetaminophen to a 95% removal rate. An increase in the reaction temperature results in a decline in the reaction rate, and this, in turn, confirms that the reaction system is exothermic in nature. The sustainability of the catalyst was verified and deemed adequate in treating and oxidizing acetaminophen, even up to the fourth cycle, achieving a 69% removal rate. A kinetic modeling approach is applied to the experimental results, and the kinetic data reveal that the oxidation system conforms to second-order kinetics, with rate constants ranging from 0.0157 to 0.0036 L/mg·min. Furthermore, an analysis of the thermodynamic parameters reveals that the reaction is exothermic and non-spontaneous, predicting an activation energy of 36.35 kJ/mol. Therefore, the proposed system can address the limitations associated with the homogeneous Fenton system.