In this paper, the influence of lactic acid fermentation on the metabolic profile of ginkgo kernel juice was studied. For this purpose, three lactic acid bacteria (LAB), Lactobacillus acidophilus, Lactobacillus plantarum and Lactobacillus casei, were selected. The results showed that all the lactobacilli grew well in ginkgo kernel juice with viable cell counts exceeding 8.0 Log CFU/mL. The organic acid contents underwent dynamic changes, and the lactic acid production reached more than 3 g/L. The consumption of sugars and free amino acids by LAB was evident. Meanwhile, more than 70% of the ginkgolic acids were degraded by LAB, and the final concentrations in ginkgo kernel juice were below 1 mg/L after 48 h of fermentation. In contrast, the terpene lactones contents in fermented ginkgo kernel juice exceed 20 mg/L, which was 1.6-fold higher than that in the unfermented juice. Certain phenolics were significantly enriched, and the total phenolic content increased by approximately 9% through fermentation. In addition, lactic acid fermentation significantly enhanced the antioxidant and anti-microbial activities of ginkgo kernel juice. Overall, the results indicated that lactic acid fermentation can effectively improve the nutritional value and safety of ginkgo kernel juice.