The design and use of innovative treatment processes are very important in preventing the possible toxic effects of organic pollutants in aquatic environments. One of these methods is the subcritical water oxidation method, which has been used recently. In the current study, the mineralization of clofibric acid (CFA) was carried out under more effective and mild conditions using persulfate (PS) as an oxidant and CoFe2O4@SiO2 catalyst by the subcritical water oxidation (sub-CWO) process. Characterization of the synthesized catalyst was performed through XRD, FTIR, TEM and SEM–EDS analyses. In the CFA oxidation with persulfate-promoted catalytic Sub-CWO process, optimum working conditions was determined as 15 mM PS, 40 min, 383 K, and 0.3 g L−1 catalyst dosage using the response surface method and Box–Behnken design. The catalyst's efficiency remained relatively stable after three cycles under optimal conditions, resulting in a 97% total organic carbon (TOC) removal. Decomposition products were determined and a degradation mechanism was proposed.