Friction stir processing (FSP) is an effective surface-microstructure modification technique using a rotational tool to refine and homogenize microstructure of metallic materials. In this study, FSP was conducted on the surface of the heat-affected zone (HAZ), which is a region exhibiting degraded mechanical properties and shown to have microstructural changes, of butt-welded joints for two high-strength steels with tensile strength grades of 490 MPa and 780 MPa (hereafter HT490 and HT780, respectively). Inhomogeneous mixing of materials derived from weld metals and base metals (BMs) in a stir zone (SZ) produced inhomogeneous distribution of elements and microstructure depending on the set of the advancing side and retreating side in the SZs. The welded joints with FSP for HT490 exhibited higher hardness than that of the BM through whole of the SZ surface (fine polygonal ferrite grains and bainite structure with laths at the Mn-rich and Mn-poor regions, respectively). On the other hand, those for HT780 exhibited the minimum hardness value similar to that of the BM at the SZ surface (a few polygonal ferrite grains in the matrix of martensite laths). Fatigue strength increased by about 35 MPa and 15 MPa in stress amplitude at 10 7 cycles as fatigue limit due to FSP. Fatigue failure occurred at the BM and the SZ, respectively, in the welded joints modified by FSP for HT490 and HT780, in comparison with the HAZs in the as-welded joints for both grade steels. The difference in fatigue strength increase due to FSP and failure location between the welded joints for HT490 and HT780 can be attributed to the topmost SZ microstructures and their distribution.