A high-speed counter-current chromatography system (HPCCC) capable of rapid processing has been employed to separate seven flavonoids from a methanolic extract of the leaves of Oroxylum indicum by a one-step isocratic elution using a chloroform–methanol–water (9.5:10:5) two-phase system. LC, MS and NMR have identified the components from the extract as chrysin, baicalein, baicalein-7-O-glucoside, baicalein-7-O-diglucoside, chrysin-7-O-glucuronide, baicalein-7-O-glucuronide, and a chrysin-diglucoside. Baicalein-7-O-glucuronide and chrysin-7-O-glucuronide have been separated from this plant by HSCCC for the first time. The present study also reports a new chrysin-diglucoside from the leaf extract. The results demonstrate that HSCCC is a powerful separation tool and can contribute to identifying and quantifying plant ingredients.