Ginsenosides are responsible for the pharmacological and biological activities of ginseng. In this study, ginsenoside Rh1 and compound K were isolated and purified from fermented ginseng substrate and their anti-allergic effects were assessed in compound 48/80-induced anaphylactic shock model. The fermented ginseng substrate was extracted by methanol and ginsenoside Rh1 and compound K were efficiently purified by preparative high performance liquid chromatography (prep HPLC). Their quality and quantity were analyzed by liquid chromatography-mass spectrometer (LC-MS) and HPLC. Ginsenoside Rh1 showed better anti-allergic effects than compound K in compound 48/80-induced anaphylactic shock model. This study suggested that fermented ginseng extracts with enriched Rh1 may be utilized as a potential biomaterial of functional food for the alleviation of allergic symptoms.