In this study, Ginkgo biloba products used for the same purpose, but licensed to varying authorities were analyzed in point of similarity to each other. A group of these products were licensed from health authorities as herbal medicinal product (HMP), while the other groups of products were licensed as the food supplement (FS). The evaluation of their phytoequivalence was carried out comparing the chromatographic fingerprint profiles. Furthermore, ginkgolides (ginkgolides GA, GB, GC, and GJ) and flavonoid aglycones (quercetin, kaempferol, and isorhamnetin) were quantitatively analyzed by using liquid chromatography-mass spectrometry (LC-MS) and HPLC-diode Array detector (HPLC-DAD) assays. All six herbal medicinal products and two food supplements were found to be phytoequivalent to each other, but five of the seven food supplements did not possess similar content as herbal medicinal products, and the quantity of ginkgolides and flavonoid aglycones per tablet/capsule was found to be lower than declared on the labels. In addition, food supplements were found to be adultered with rutin to reach expected total flavonoid glycosides amount.