In this work the separation of eighteen flavonoids was attempted using reduced-flow micellar elektrokinetic chromatography (RF-MEKC) electrolytes modified by selected solvents with differing properties: methanol (MeOH), acetonitrile (ACN) and tetrahydrofuran (THF). Structural aspects such as unsaturation of the C ring, number and position of OH groups, methylation and glycosylation as well as solvent effects and their impact on the electrophoretic behavior of flavonoids were addressed. By evaluating the electropherograms obtained from mixture-designed electrolytes and searching for changes in the critical pairs, a favorable separation condition was achieved using 20 mmol/L phosphate buffer at pH 2.5 containing 50 mmol/L sodium dodecyl sulfate (SDS), 15% ACN and 5% THF (one critical pair) in less than 12 min with 1.5% coefficient of variation (CV) for retention factor and 3% CV for peak area (n = 5). The applicability of the proposed separation condition was demonstrated by the inspection of flavonoids in herbal extracts of Neem.