Bilberry fruit extracts have been used as herbal medicines for the treatment of vascular and vision disorders in Europe, whereas they are only used in health food products in Japan. In April 2015, “Foods with Functional Claims (FFCs)” was established as a new category of voluntary labeling in health food products sold in Japan, and several bilberry-containing products have been submitted as FFCs. To ensure the efficacy and safety of the FFCs, effective quality control on the original plants, consistent composition, and manufacturing process is important for the herbal ingredients with specific health-related functions. In this study, we evaluated the quality and quantity of 5 FFCs whose functional substances are bilberry anthocyanins. Twenty compounds (15 anthocyanins and 5 anthocyanidins) in the FFCs were separated by the HPLC method according to the European Pharmacopoeia instead of the journal featuring dietary supplements. Cyanidin-3-rutinoside was detected in 3 FFCs containing black currant extracts as well as bilberry extracts, and the anthocyanins in these FFCs were considered to be derived from both plants. Since the bilberry extracts are the active ingredient with pharmaceutical evidence and its health benefits are displayed on the product’s packaging, the proper regulation for ensuring a consistent quality of bilberry-containing FFCs would be recommended.