<p>Geogenic inputs have become a vital source for rare earth elements (REE) in the surrounding environments with black shale outcrops. However, the geochemical fractionation and differential accumulation of REE in the rock-soil system of black shale regions still remain unclear. Therefore, this study performed a typical sampling of paired bedrocks and soils in contrasting topographies in a black shale catchment in southwestern China to characterize the geochemical enrichment and fractionation of REE during black shale weathering and soil formation and evolution. The results indicate that black shale bedrocks have elevated total concentrations of REE compared to the North American Shale Composite and the Upper Continental Crust; while surface soils have total REE concentrations higher than the Chinese soil background value. The contrary REE distribution patterns for upland soils (concave-up) and lowland soils (convex-up), together with a higher (La/Sm)_N value (1.11 ± 0.18) and a lower (Gd/Yb)_N value (1.13 ± 0.11) in the upland soils and a lower (La/Sm)_N value (0.95 ± 0.11) and a higher (Gd/Yb)_N value (1.32 ± 0.31) in the lowland soils, indicate the obvious fractionation of REE between the two soil types and the preferential enrichment of MREE (and HREE) in the lowland soils, which was attributed to the release of MREE (and HREE) from the weathering of upland black shale bedrocks and their downward translocation by water fluxes and subsequent precipitation in lowlands. In addition, the lowland soils are more enriched in LREE than the upland soils, which should be associated with the downward transportation of LREE-rich mineral particles caused by soil erosion on the hillslope. Overall, this study points out that MREE enrichment in the lowland soils of black shale regions and its associated health risks should be noticed.</p>