Diazonium salts, which selectively functionalize metallic single-walled carbon nanotubes (SWNTs) over semiconducting in SWNT mixtures, exhibit a negative charge upon being exposed to a highly basic solvent. We applied this selective chemistry for separating the functionalized SWNTs from non-functionalized, using a electro-diffusion mechanism. The SWNT mixtures, in which metallic SWNTs were selectively functionalized over semiconducting by 4-hydroxybenzene diazonium salts, were separated into two fractions, one remained where the mixtures were injected (center fraction) and the other moved to the positive electrode (positive fraction) under the electric field, depending on the extent of functionalization. UV-Vis absorption spectra and the changes of area ratio for disorder over tangential mode in 633nm-Raman spectra revealed that the positive fraction was enriched in functionalized SWNTs, while the center fraction was enriched in non-functionalized. Since the metallic SWNTs are preferentially functionalized over semiconducting with diazonium salts, SWNT mixtures can be separated using this novel electro-diffusion method.