In this study, edible protopanaxadiol saponin enriched fraction were prepared by ultrafiltration (UF). Ginseng extract was prepared from mixtures of ginseng main root and rootlet (root: rootlet = 4 : 6). UF system was used the four-piston Diaphragm pump equipped with 5 kDa pore size Hydrosart Cassette made by regenerated cellulose acetate (CA) or 3 kDa pore size Hollow Fiber cartridge made by polyethersulfone (PES). Total ginsenoside contents of concentrated fraction by UF system was found to higher, compared to before those of untreated method. Especially, processing of UF showed the increase of PPD-type ginsenoside, while PPT-type ginsenoside was gradually decreased by both 3 kDa and 5 kDa membrane. After removal of 80% water by the 5 kDa Hydrosart Cassette and by 3 kDa Hollow Fiber cartridge, ginsenoside Rb1 content was higher 37.2 mg/g and 25.3 mg/g than 20.8 mg/g in untreated process. The ratio of Rb1 to Rg1 (Rb1/Rg1) and PPD- to PPT- type ginsenoside (PPD/PPT) were higher in inner fluid of ginseng extract after UF by 3 kDa cartridge (47.1 and 23.5, respectively) and 5 kDa Cassette (25.3 and 11.9, respectively) than those of before UF (5.7 and 3.7, respectively). PPD-type ginsenoside enriched fraction by UF system could be developed as a new ginseng material in food and cosmetic industrials.