The expansion in the use of rare earth elements (REEs) in last decades has led to the emergence of the problem of soil pollution with these elements and their ecological risk. This research aims to assess soil pollution with REEs in Aswan and Luxor districts, Egypt, and their ecological risk. Agricultural soil samples were collected and prepared for mineralogical and chemical investigation. Pollution indices were applied to investigate the degree and hazard of the occurrence of these elements in the study areas. Mineralogically, the studied soils composed of montmorillonite and kaolinite as clay minerals as well as quartz and calcian-albite. The recorded average ƩREEs concentration was 160.8 and 248.3 µg/g for Aswan and Luxor; respectively. Both regions have the same trend, Ce is the highest recorded element and Pr is the lowest. The REEs are most probably derived from the phosphate fertilizers and/or Phosphate Mining in El Sebayia. In addition, Sc and Sm are weakly correlated with Al and Fe which indicated that the clay minerals can be play a significant role in their mobilization, as well as iron has the capability of scavenge them in the studied soils in Luxor and Aswan governorates. The contamination factor indicated the low contamination with La and Nd, moderate contamination with Ce, Pr, Sc and Y, as well as considerable contamination with Sm. Gurna and Habo soils (Luxor Governorate) recorded high concentration of REEs than which in Aswan Governorate. REEs haven't ecological risk in the study areas. Finally, a detailed baseline study about the distribution of potential toxic elements in the Egyptian environmental constituents (soil, water, air and plant) must be done.