In this paper, a micellar electrokinetic chromatographic (MEKC) method using ionic liquid as modifier for the quantification of the active components of lignans found in the medicinal herbs Schisandra species was developed for the first time. Preliminary investigations employing sodium dodecyl sulfate (SDS) as surfactant did not lead to the necessary resolution of the studied compounds, the addition of ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM-BF4) to the SDS micellar system resulted in the complete separation of all the compounds. The effects on the separation by several parameters such as BMIM-BF4 and SDS concentration, applied voltage, background electrolyte pH and concentration, were evaluated. Under the optimal conditions (5 mM borate-5 mM phosphate buffer in the presence of 20 mM SDS and 10 mM BMIM-BF4, pH 9.2, applied voltage 25 kV and detection at 254 nm), the method successfully applied to the determination of lignans in extracts of Schisandra chinensis (Turcz.) Baill. and Schisandra henryi C.B. Clarke in less than 13 min. The separation mechanism was also discussed.