The selective permeation of Nd through an RE–Ni (RE = Nd and Dy) alloy diaphragm was investigated in LiCl–KCl eutectic melts containing NdCl3 and DyCl3 or LaCl3 at 450 °C. The investigation was a part of an ongoing study on a new recycling process for Nd–Fe–B permanent magnets. Selective permeation of Nd was achieved by controlling the potential of the alloy diaphragm, which functioned as a bipolar electrode. Interestingly, energy dispersive X-ray analysis revealed that the Nd content in the alloy diaphragm was less than 2 at%. These results suggest that the transportation rate of Nd atoms in the alloy diaphragm was extremely high compared to that of Dy atoms. To obtain further insights into the transportation mechanism of the RE atoms in the alloy diaphragm, transmission electron microscopy (TEM) was performed. The TEM results suggest that the transportation of RE atoms cannot be explained only by simple grain boundary diffusion, and that a large number of dislocations formed in the alloy diaphragm contribute to the rapid transportation of the RE atoms.