This study investigated the impacts of two different health claim regulatory systems, FoSHU (Foods for Specified Health Uses) and FFC (Foods with Function Claims) systems, in Japan on consumer evaluations of food products in terms of healthfulness. The FoSHU system was introduced in 1991 as an individual product approval system to allow product-specific health claims, while the FFC system was introduced lately in 2015 as a notification system like NLEA (Nutrition Labeling and Education Act) in the US. The latter system seems advantageous over the former in terms of shortening the product development period. However, the FoSHU system awards brand with a symbolic logo designed for FoSHU foods, whereas the FFC system does not. Which system leads to higher consumers’ healthfulness perceptions? The results of ANOVA showed that, if the health functions of the food product are not attributed to the product category, but to a specific food product brand, health claims have a strong impact on healthfulness. In contrast, if the health functions are attributed to the entire product category, health claims do not have a strong impact on healthfulness perception. In the latter cases, the FoSHU symbolic logo helps consumers to identify functional foods. Thus, in this study, it is suggested that, in Japan, the new US style health claim regulatory system is affective in the limited product categories. Public policy makers should recognize the important role of the symbolic logo for the previous system and consider introducing another logo to the new system.