Synthesized nanoparticles often require fine fractionation according to shape, dimension, mass, chemical composition, charge, and other properties in order to become suitable for practical use. Quantum dots (QDs) are luminescent nanocrystals with narrow emission peaks. This property has been widely utilized for the multiplexed sensing and barcoding of microparticles. QDs with narrower emission peaks are preferred for such applications. The width of the emission peaks can be significantly reduced after purification. A newly developed preparative isotachophoretic method employs the dependence of spectral properties and electrophoretic mobility on the diameter of QDs. Separated fractions of QDs revealed narrower emission peaks (72% of the original width) and improved quantum yield (two-fold). The usefulness of the developed isotachophoresis for purification and analysis of other nanostructures, for example, plasmonic nanoparticles and nanobioconjugates, is expected, too.