Fluoroquinolones are extensively used in medicine due to their antimicrobial activity. Their presence in water inhibits microorganism activity in conventional wastewater treatment plants. This study aims to evaluate the technical feasibility of applying heterogeneous catalytic ozonation to eliminate ciprofloxacin (CIP) as a representative of fluoroquinolone antibiotics normally present in municipal wastewater discharges. Experiments were conducted in a semi-batch stirred slurry reactor, using 0.7 L of 100 mg L−1 CIP aqueous solution, at pH 3 and 30 °C. Experimental results show that single ozonation can easily oxidise CIP molecules (68%) within the first 5 min, leading to the generation of refractory oxidation by-products. However, when heterogeneous catalytic ozonation is applied using iron oxide supported on MFI synthetic zeolite, total degradation of CIP is observed at 5 min and a higher mineralisation rate is obtained. A novel sequential process is developed for CIP mineralisation. In a first step, a flash single ozonation is applied and CIP molecules are broken down. Then, a catalytic ozonation step is conducted by adding the Fe/MFI catalyst into the reactor. As a result of catalyst addition, 44% of Total Organic Carbon (TOC) is eliminated within the first 15 min, compared to single ozonation where only 13% of TOC removal is reached in the same time. The application of this sequential process to a real wastewater effluent spiked with CIP leads to 52% of TOC removal.