The distribution of rare earth elements (REEs) within fossil bones is controlled by their partition coefficients between apatite and pore waters, and the rate of diffusion through the bone. Using simple theoretical models, we show that REEs are strongly fractionated from one another during diffusive transport and adsorption. Fractionation occurs due to the relative ease of substituting REE ions of differing ionic radius into the Ca sites in the apatite lattice, and the degree of fractionation is dependent on the rate of diffusion of ions within bone (and therefore the rate of recrystallisation). Variations in bone thickness, recrystallisation rate, and potentially pore water composition may all influence the relative distribution of REEs, and thus REE ratios within bones. Increases in bone thickness and reductions in either diffusion coefficients or the duration of REE uptake lead to enhanced fractionation of REEs in our model simulations. Interpretations of REE ratios in fossil bones either for palaeoenvironmental or taphonomic applications must consider how fractionation will influence REE ratios within bones, particularly when interpreting spatially resolved analyses within single bones.