Carbendazim (CBZ), a widely used fungicide in agriculture, is frequently detected in aquatic environment and causes significant concerns because of its endocrine-disrupting activity. This study investigated the degradation kinetics of CBZ in ferrate (Fe(VI)) oxidation, the influence of water matrices, and the transformation pathways of CBZ. The second-order rate constant for the reaction between CBZ and Fe(VI) decreased from 88.0 M−1·s−1 to 1.6 M−1·s−1 as the solution pH increased from 6.2 to 10.0. The optimum reaction conditions were obtained through response surface methodology, which were pH = 7.8 and [Fe(VI)]/[CBZ] = 14.2 (in molarity), and 96.9% of CBZ could be removed under such conditions. Cu2+ and Fe3+ accelerated the degradation of CBZ by Fe(VI) oxidation; common cations and anions found in natural water had no significant effect, while the presence of humic acid also accelerated the degradation of CBZ. Based on the degradation products identified, degradation of CBZ in Fe(VI) oxidation proceeded via three pathways: namely, hydroxylation, removal of the methoxyl group, and cleavage of the C–N/C=N bond. The initial reaction site of CBZ oxidation by Fe(VI) was also supported by the atomic partial charge distribution on the CBZ molecule obtained from density functional theory (DFT) calculations. CBZ in natural water matrices was efficiently removed by Fe(VI) oxidation under near-neutral conditions, indicating that Fe(VI) oxidation could be a promising treatment option for benzimidazole fungicides.