Calcium atoms are often replaced by rare earth elements (REEs) in the lattice of fluorapatite (Ca10F2(PO4)6), making the phosphate ore an important potential rare earth resource. In this paper, the electronic properties of REEs (La, Ce, Nd and Y) bearing fluorapatite crystals have been investigated by density functional theory. Results of calculation indicated that the existence of REEs increased the cell parameters of fluorapatite in varying degrees. The REEs substitution made the Fermi level of fluorapatite to move to higher energy levels, making it easier to accept electrons. Except for Y, all the other REEs (La, Ce and Nd) showed that the electronic state mainly exists in the valence band. The Fermi level of REEs were mainly contributed by La5d, Ce4f, Nd4f and Y4d, respectively. The Mulliken values of REE–F and REE–O bonds in REEs-bearing fluorapatites were larger than those of Ca–F and Ca–O bonds in the perfect crystal, and the values of Y–F and Y–O bonds were the largest. The results of interaction between fluorapatite and oleic acid by frontier molecular orbital analysis suggested that the substitution of REEs can improve the reactivity of fluorapatite with oleic acid.