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<i>Uraria crinita</i> is used as a functional food ingredient. Little is known about the association between its immunomodulatory activity and its metabolites. We applied a precise strategy for screening metabolites using immunomodulatory fractions from a <i>U. crinata</i> root methanolic extract (UCME) in combination with bioactivity-guided fractionation and NMR-based identification. The fractions from UCME were evaluated in terms of their inhibitory activity against the production of pro-inflammatory cytokines (IL-6 and TNF-<i>&#945;</i>) by lipopolysaccharide (LPS)-stimulated mouse bone marrow-derived dendritic cells (BMDC). The role of the isoflavone genistein was indicated by the ¹H NMR profiling of immunomodulatory subfractions (D-4 and D-5) and supported by the result that genistein-knockout subfractions (D-4 <i>w</i>/<i>o</i> and D-5 <i>w</i>/<i>o</i>) had a lower inhibitory activity compared to genistein-containing subfractions. This study suggests that genistein contributes to the immunomodulatory activity of UCME and will help in the standardization of functional food.