Response of growth and secondary metabolites to light intensity are useful measurements to determine suitable silviculture treatments for the cultivation of medicinal plants. Here, we analyzed the growth, flavonols (total flavonol, quercetin, kaempferol, and isorhamnetin) content, flavonols yield per plant, and expression of flavonoid biosynthesis-related genes in 2-year Ginkgo (Ginkgo biloba L.) seedlings at four different light intensities (100, 76, 40, and 25 % of full sunlight) in a greenhouse setting. Across all light intensities, the 76 % sunlight treatment produced the highest growth of total biomass, root, stem, and leaf, indicating negative effects of either fulllight or heavy shading on Ginkgo seedling development. Both flavonols (total flavonol, quercetin, kaempferol, and isorhamnetin) content and expression of flavonoid biosynthesis-related genes [PAL (Phenylalanine ammonia-lyase), CHS (Chalcone synthase), F3H (Flavanone 3-hydroxylase), and FLS (Flavonol synthase)] in leaves were highest under 100 % sunlight, suggesting that full sunlight promotes the expression of flavonoid biosynthesis-related genes and increases flavonoid biosynthesis. The highest and lowest flavonol contents were found in leaves and stems, respectively. The 76 % sunlight treatment produced the highest flavonols yield while the 100 % sunlight produced the highest flavonoids content in leaves, indicating that flavonol production per unit land area depends not only flavonol content but also biomass. Overall, in order to achieve the highest flavonols yield per area in Ginkgo leaf-harvesting plantations, it is important to manipulate light conditions of field.