An ethanol extract of air-dried flowers of Edgeworthia chrysantha Lindl. was partitioned between water and petroleum, ethyl acetate, and n-butanol. The n-butanol extraction was initially purified by silica gel column chromatography to give a partially purified sample. The bioactive compound rutin, along with nicotiflorin, were successfully separated from the partially purified sample by high-speed counter-current chromatography. The two compounds were isolated from the plant of Edgeworthia genus for the first time. The two-phase solvent system used was composed of ethyl acetate-n-butanol-water at an optimized ratio of 4:1:5 (v/v/v). High-speed counter-current chromatography yielded, from 108 mg of the partially purified extract, 53 mg rutin and 32 mg nicotiflorin with 92.5% and 92.2% recovery, with each at over 96.5% purity by high-performance liquid chromatography analysis. Their structures were identified by 1H NMR and 13C NMR.