In the present study, a high-speed counter-current chromatography (HSCCC) was investigated for separation and purification of gardecin on a preparative scale. Hexane-ethyl acetate-methanol-water (0.3:1:0.3:1, v/v) was selected as the optimum solvent system to purify gardecin from a fraction obtained from HPD100 column chromatography fractionation of gardenia. After HSCCC isolation, 20.1 mg of gardecin with purity of 97.4% was obtained from 322 g of dry gardenia fruits. Chemical structure identification of this pigment was carried out by MS, H-1 NMR, and C-13 NMR. Additionally, antioxidant activity of gardecin in comparison with crocin-1 was investigated. The present results demonstrated that gardecin could be efficiently obtained using HSCCC from this herb and this compound features strong antioxidant activity.