This paper evaluates the oxidation of an antibacterial agent, chlorophene (4-chloro-2-(phenylmethyl)phenol, CP), by permanganate (Mn(VII)) in water. Second-order rate constant (k) for the reaction between Mn(VII) and CP was measured as (2.05 ± 0.05) × 101 M−1 s−1 at pH 7.0 for an initial CP concentration of 20.0 μM and Mn(VII) concentration of 60.0 μM. The value of k decreased with increasing pH in the pH range of 5.0–7.0, and then increased with an increase in solution pH from 7.0 to 10.0. The presence of MnO2 and Fe3+ in water generally enhanced the removal of CP, while the effect of humic acid was not obvious. Fourteen oxidation products of CP were identified by an electrospray time-of-flight mass spectrometer, and direct oxidation, ring-opening, and decarboxylation were mainly observed in the reaction process. The initial reaction sites of CP by Mn(VII) oxidation were rationalized by density functional theory calculations. Toxicity changes of the reaction solutions were assessed by the luminescent bacteria P. phosphoreum, and the intermediate products posed a relatively low ecological risk during the degradation process. The efficient removal of CP in secondary clarifier effluent and river water demonstrated the potential application of this Mn(VII) oxidation method in water treatment.