Friction stir processing (FSP), as a new kind of severe plastic deformation technique, can refine and homogenize the microstructure of metallic material. In this study, the effect of FSP on the microstructure and mechanical properties of pure Zr was investigated using electron backscatter diffraction analysis, microhardness and room-temperature tensile testing. The fine-grained (FG) structure with an average grain size of ~ 5.3 μm was obtained in the processed zone, where the average microhardness was ~ 198 HV, 1.6 times higher than that of base metal. Furthermore, tensile property of FG pure Zr exhibited obvious anisotropy owing to strong texture. Both grain size and texture had a significant effect on strength and ductility of FG pure Zr. High yield strength (248 MPa) and ultimate tensile strength (483 MPa), as well as good uniform elongation (10%) were achieved, which demonstrated that FSP was an effective method to fabricate bulk FG pure Zr with high strength and good ductility.