We determine the proper placement of the reference electrode for impedance measurements in lithium-ion rechargeable batteries with a three-electrode cell. Calculations of the impedance spectra of the positive and negative electrodes and simulations of the current and potential distributions between them are performed using the finite element method. In the simulation, the positive and negative electrodes are symmetrical face to face. Distortions of the loops and artifact inductive loops are observed in the impedance spectra of the positive and negative electrodes when the reference electrode is between or at the edges of the electrodes. These distortions and the diameter of the artifact inductive loops become small when the reference electrode is positioned outside the area between the positive and negative electrodes. Simulations also demonstrate that current from the positive electrode can flow to the reference electrode and then the negative electrode, i.e., part of the reference electrode facing the positive electrode becomes cathode and part of the reference electrode facing the negative electrode becomes anode. Therefore, the dissolution of reference electrode occurs during impedance measurements in a three-electrode cell and the reference electrode should be placed outside of the area between electrodes, where there is no potential modulation and gradient.