The minor ginsenosides with less polarity may have more potent biological activities. Four minor saponins, i.e., gypenoside XVII, ginsenoside Rd2, notoginsenoside Fe, and notoginsenoside Fd, were successfully separated from Panax notoginseng leaves (PNL) after biotransformation by one-step countercurrent chromatography using the biphasic solvent system consisting of n-butanol–ethyl acetate–water (1:4:5, v/v/v). 30 mg of the refined extract of PNL produced 1 mg of gypenoside XVII, 4 mg of notoginsenoside Fe, 2.5 mg of ginsenoside Rd2, and 8.4 mg of notoginsenoside Fd, with purity of 74.9, 95.2, 87.3, and 97.6%, respectively. Besides, orthogonality evaluation for the separation of the four saponins using countercurrent chromatography and liquid chromatography was discussed. Four minor saponins were successfully separated from each other on a preparative scale by countercurrent chromatography from PNL, which will facilitate to provide ample of these minor saponins for further pharmacological studies.