The fabrication of a hydrogen isotope enrichment system is essential for the development of industrial, medical, life science, and nuclear fusion fields, and therefore, efficient enrichment techniques with a high separation factor and economic feasibility are still being explored. Herein, we report a hydrogen/deuterium (H/D) separation ability with polymer electrolyte membrane electrochemical hydrogen pumping (PEM-ECHP) using a heterogeneous electrode consisting of palladium and graphene layers (PdGr). By mass spectroscopic analysis, we demonstrate significant bias voltage dependence of the H/D separation factor with a maximum of ∼25 at 0.15 V and room temperature, which is superior to those of conventional separation methods. Theoretical analysis demonstrated that the observed high H/D factor stems from tunneling of hydrogen isotopes through atomically thick graphene during the electrochemical reaction and that the bias dependence of H/D results from a transition from the quantum tunneling regime to the classical overbarrier regime for hydrogen isotopes transfer through the graphene. These findings will help us understand the origin of the isotope separation ability of graphene discussed so far and contribute to developing an economical hydrogen isotope enrichment system using two-dimensional materials.