We present the effect of pulsed direct current on metal ion diffusion in CaB6–SrB6 diffusion couples, showing that the diffusivity of Ca2+ and Sr2+ across the diffusion couple interface is higher toward the positive electrode when subjected to a current flow of 2.2 kA at a temperature of 2007 K. We attribute this enhanced mobility to the movement of negatively charged metal vacancies toward the positive electrode in the system. Energy-dispersive spectroscopy is used to map the concentration of Ca2+ and Sr2+ in the region near the interface, and diffusion profiles are fitted with error functions. The concentration curves display concentration-dependent Boltzmann–Matano diffusivity. Total dopant values (Q) have been used to numerically compare the differences between Ca2+ diffusion in SrB6 and Sr2+ diffusion in CaB6. We determine an enhancement of 3.8× for Ca2+ into SrB6 versus an enhancement of 1.8× for Sr2+ into CaB6. No new phases are formed at the interface between CaB6 and SrB6, since hexaboride compounds readily form solid solutions. The results elucidate the role of pulsed direct current on the diffusion of metal ions in hexaboride compounds.