The bioactive component harpagoside was successfully separated from the crude extract of Scrophularia ningpoensis Hemsley by one-step purification using high-speed counter-current chromatography (HSCCC). A two-phase solvent system containing n-butanol:ethyl acetate:water (1:9:10) was selected following consideration of the partition coefficient of the target compound. A 276 mg quantity of the crude extract was loaded onto a 250 mL HSCCC column and yielded 11 mg harpagoside at over 97% purity. The chemical structure of harpagoside was determined by HPLC-ESI/MS and 1H-NMR.