The objective of this study was to investigate the fermentation mechanism of ginkgo kernel juice (GKJ) under unfermented (Group A), Ginkgolide B (GB)-producing Lactiplantibacillus plantarum fermented (Group B), and co-induced fermented (Group C) conditions. The conditions were optimized and further evaluated for their vascular endothelial cell protective effects in vitro. The co-induced fermented GKJ group extensively promoted GB and total phenol contents, reaching 109.94 and 599.57 μg/mL, respectively. While pH declined from 5.90 to 3.42 during fermentation, the highest total viable count (8.85 log CFU/mL) was detected at 16 h in the L. plantarum group. The co-induced group recorded the highest total phenol contents (594.05 μg/mL) and markedly induced the survival rate, reactive oxygen species formation, and lactate dehydrogenase assay cytotoxicity of H2O2-induced human umbilical vein endothelial cells. An untargeted metabolomics analysis identified 2633 metabolites in the groups. The principal component and orthogonal partial least squares discriminant score plots showed a clear metabolite distinction among the fermentation groups. From the Kyoto Encyclopedia of Genes and Genomes analysis, 309 differential accumulated metabolites (DAMs) were up-regulated and 604 were down-regulated in the A vs. B group, while 702 downregulated and 304 upregulated DAMs were exhibited in the B vs. C group. These DAMs were primarily lipids and lipid-like molecules, organic acids and their derivatives, organoheterocyclic compounds, organic oxygen compounds, benzenoids, phenylpropanoids and polyketides, and unclassified compounds at the superclass level. Overall, the results indicated that L. plantarum and co-induced fermentation improved the cell protection efficacy of GKJ, showing excellent potential for drug delivery applications.