This research has been focused on the removal of two anti-inflammatory drugs, diclofenac (DCF) and ibuprofen (IBU), by a continuous catalytic wet peroxide oxidation (CWPO) process using a lab-synthesized nanomagnetic catalyst (Fe3O4/MWCNTs). The central composite rotatable design (CCRD) method was used to study the effect of DCF and IBU concentration (expressed as theoretical oxygen demand (ThOD) between 0 and 52.5 mg L−1) and of the feed stream pH (from 3 to 7) on the removal of total organic carbon (TOC) and the concentration of aromatic compounds (Arm) and total phenolic compounds (TP) by CWPO. It could be observed that DCF was preferably removed from the DCF-IBU aqueous mixture at pH values ranging from 3 to 5. In addition, feed stream pH had a significant effect on the pollutants removal, as well as on TOC, TP and aromatic compounds removal, observing an increasing in the pollutants degradation when feed stream pH decreased from 7 to 3. Quadratic models predicted for response variable, such as TOC, TP and aromatic compounds removal, and their maximum model-predicted removal values were of 90.0, 80.2 and 90.0%, respectively. Finally, as a proof of concept, three environmentally-relevant aqueous matrices, spiked with DCF-IBU mixture, were treated. In this case, relatively high TOC degradation values were found after 20 h reaction time (ca. 57.7, 73.9 and 54.5% in surface water, WWTP effluent and hospital wastewater, respectively). This work deals the first study about DCF-IBU removal in aqueous solution by CWPO, as well as a continuous study using real wastewater that allow to extend the experimental results to a real scenario.