Ginkgo biloba (Ginkgoaceae), well-known as the oldest living plant species and often referred to as a “living fossil,” is a famous medicinal plant that has been used in multiple countries to improve numerous illnesses, including anxiety, dementia, peripheral artery disease, and eye problems. We conducted a phytochemical exploration of G. biloba fruit, commonly consumed as a functional food as part of an ongoing natural product chemical research for the discovery of bioactive phytochemicals with novel structures. The natural product chemical analysis of the methanol extract of G. biloba fruit using column chromatography and high-performance liquid chromatography separation under the guidance of a liquid chromatography–mass spectrometry (LC/MS)-based analysis identified six phenylpropanoid glycosides (1–6), including one new compound, ginkgopanoside (1). The structures of the isolated compounds were elucidated by nuclear magnetic resonance spectroscopic data and LC/MS analysis, and the absolute configuration of compound 1 was established by chemical reactions followed by the application of Snatzke’s method. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activities of the isolated compounds 1–6 and the aglycone 1a of 1 were evaluated, and we found that compounds 1–5 exhibited antioxidant activities with IC50 values in the range 32.75–48.20 M, while the aglycone 1a exhibited greater radical scavenging activity (IC50 = 5.23 M) comparable to that of ascorbic acid (IC50 = 2.54 M), a positive control, implying that the present of glucose may decrease the DPPH scavenging activity. These findings provide experimental information that the active phenylpropanoid glycosides could represent natural antioxidants for use in pharmaceuticals and functional foods.
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