An improved process for preparing tenuifolin (presenegenin 3-β-d-glucopyranoside) from the root of Polygala senega L. was developed. A crude saponin mixture extracted from P. senega was subjected to hydrolysis, and the reactivity of compounds in the extract was controlled by utilizing the combination of a flow reactor and experimental design. In addition, column chromatography with HP 20, a synthetic polystyrenic adsorbent, allowed the gram-scale preparation of tenuifolin in a continuous manner with fewer steps. This approach shortens the total time required for gram-scale preparation from 16 to 5 h in a continuous manner while improving the yield from 0.59% to 2.08% (w/w).