Analytical prospects of ionic liquids as the components of the microemulsion for polyphenols separation by microemulsion electrokinetic chromatography are explored. Imidazolium-based hydrophilic ionic liquid 1-hexadecyl-3-methylimidazolium chloride was used as a surfactant and hydrophobic ionic liquids 1-hexyl-3-methylimidazolium tetrafluoroborate and 1-hexyl-3-methylimidazolium bis(trifluormethylsulfonyl)imide were used as the oil phase. It was shown that the addition of ionic liquids into the microemulsion leads to a significant increase in the number of theoretical plates for catechins separation (in the range 200–650 ×10³) in both cases. It was established that the use of hydrophobic ionic liquids 1-hexyl-3-methylimidazolium tetrafluoroborate and 1-hexyl-3-methylimidazolium bis(trifluormethylsulfonyl)imide increases the sensitivity and selectivity of the polyphenols separation compared to 1-hexadecyl-3-methylimidazolium chloride. The following composition of microemulsion was found to be optimal for the selective electrophoretic separation of catechins with ionic liquids as the oil phase: 0.6% (w/v) sodium dodecyl sulphate, 0.7% (w/v) 1-hexyl-3-methylimidazolium tetrafluoroborate, 1.6% (w/v) 1-butanol, 5 mM phosphate buffer solution, pH = 7. The conditions for the electrophoretic separation of catechins with microemulsion electrokinetic chromatography were used to determine polyphenols in tea samples.