The impact of rare earth oxide (REO) concentration on the deposition process and selective recovery of the metal being deposited from a molten fluoride salt system was investigated by applying deposition of Nd and Pr and varying the concentration of REO added to the electrolyte. A ternary phase diagram for the liquidus temperature of the NdF3-PrF3-LiF system was constructed to better predict the optimal electrolyte constitution. Cyclic voltammetry was used to record three redox signals, reflecting the processes involving Nd(III)/Nd and Pr(III)/Pr transformations. A two-step red/ox process for Nd(III) ions and a single-step red/ox process for Pr(III) ions were confirmed by square-wave voltammetry. The cyclic voltammetry results indicated the possibility of neodymium and praseodymium co-deposition. In order to sustain higher co-deposition rates on the cathode and to avoid increased production of PFC greenhouse gases on the anode, a low-overpotential deposition technique was used for Nd and Pr electrodeposition from the electrolyte with varying Nd2O3 and Pr6O11 concentrations. Co-deposited neodymium and praseodymium metals were characterized by electron probe microanalysis (EPMA) and X-ray diffraction (XRD) analysis. After electrodeposition, concentration profiles of neodymium and praseodymium were recorded, starting from the cathode surface towards the electrolyte bulk. The working temperature of 1050 °C of the molten fluoride salt basic electrolyte, in line with the constructed phase diagram, was validated by improved co-deposition and led to a more effective deposition process.