Isoflavones are a very important group of natural products. This study investigated the separation of eight isoflavones, namely ononin, daidzin, genistin, biochanin A, formononetin, puerarin, genistein, and daidzein, from pueraria by micellar electrokinetic chromatography (MEKC) with different surfactants. The following micellar systems of MEKC were systematically compared for the analysis of these isoflavones: (1) a single surfactant comprising the anionic surfactant sodium dodecyl sulfate (SDS), the cationic surfactant hexadecyltrimethylammonium bromide, the neutral surfactant polyoxyethylene sorbitan monolaurate (Tween 20), and the ionic liquid-type surfactant (also a cationic surfactant) 1-dodecyl-3-methylimidazolium tetrafluoroborate (CMIMBF); (2) different single surfactants with 1-butyl-3-methylimidazolium tetrafluoroborate (BMImBF) as an additive (modifier); and (3) mixed micelles of SDS + Tween 20 and CMIMBF + Tween 20. Both SDS with BMImBF as additive and mixed micelles of SDS + Tween 20 had the highest separation efficiency for the eight investigated compounds. Furthermore, the SDS with BMImBF as additive was more stable (good repeatability of retention time and peak shape of analytes) than mixed micelles of SDS + Tween 20, which may be the result of a stabilizing effect of BMImBF. Therefore, the final analytical conditions were 15 mM SDS added with 50 mM BMImBF in 30 mM sodium tetraborate (STB, pH 9.5) as running buffer; applied voltage, 20 kV; injection, 50 mbar for 5 s; cartridge temperature, 25 °C; compounds were detected at 260 nm. The developed method was fully validated (limit of detection, limit of quantification, intraday precision, inter-day precision, and recovery) and successfully applied to determine the eight analytes in three Radix Puerariae samples. The present study indicated that SDS with ionic liquids as additive in MEKC was suitable for the analysis of isoflavones.