In this paper, Fe3O4/graphene (Fe3O4/GE) nanocomposites were prepared by a co-precipitation method and characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM) and UV-vis diffuse reflectance spectra (UV-vis DRS). The composites were used in combination with Fe(VI) to construct a Fe(VI)-Fe3O4/GE system in order to degrade ciprofloxacin (CIP) in simulated water samples. The photocatalytic properties of Fe(VI)-Fe3O4/GE were evaluated under visible light irradiation. The concentration of CIP in solution was detected by high performance liquid chromatography (HPLC). A series of results showed that Fe(VI), as a good electron capture agent, could significantly improve the treatment performance. Major determining factors during CIP degradation were also investigated, in which solution pH of 9, Fe(VI) to Fe3O4/GE dosage ratio of 1:25 and GE content in the Fe3O4/GE nanocomposites of 10 wt% were found to be the best experimental conditions. The results demonstrated that the Fe(VI)-Fe3O4/GE system could offer an alternative process in water treatment in addition to the current Fe(VI)-UV/TiO2 process.