Uniform Bi2MoO6 nanosheets were grown in a high dispersed fashion on electrospun BiFeO3 nanofibers via a solvothermal technique. The loading amount of Bi2MoO6 in the Bi2MoO6/BiFeO3 heterojunction nanofibers could be controlled by adjusting the precursor concentrations in the solvothermal process. The XPS analysis, energy band position calculation and trapping experiments all proved that the Bi2MoO6/BiFeO3 heterojunction is a Z-scheme heterojunction. The Z-scheme Bi2MoO6/BiFeO3 heterojunction had a much higher photocatalytic activity in the visible-light photodegradation of Rhodamine B (RhB) and tetracycline hydrochloride (TC) than pure BiFeO3 nanofibers or pure Bi2MoO6 nanosheets. The enhanced photocatalytic activity was attributed to the formation of Z-scheme Bi2MoO6/BiFeO3 heterojunctions, which could be beneficial to the separation of photogenerated electron-hole pairs. Moreover, the Bi2MoO6/BiFeO3 heterojunction nanofibers could be easily separated under an external magnetic field via the ferromagnetic BiFeO3. After several cycles, the photocatalytic activity of the Bi2MoO6/BiFeO3 heterojunction no longer significantly decreased suggesting that the Bi2MoO6/BiFeO3 heterojunction is stable. These Z-scheme Bi2MoO6/BiFeO3 heterojunction nanofibers with highly visible-light photocatalytic activity, excellent chemical stability and magnetic separability could be useful in many practical applications.