Numerous studies have looked at sustainable tourism as the key to balancing environmental conservation and development in agricultural heritage sites. A microcosm of the traditional rural productive landscape, the Noto Satoyama Satoumi landscape has been designated as a pilot site for the Globally Important Agricultural Heritage System (GIAHS) in Japan. This paper discusses the challenges and opportunities of green tourism, focusing on the GIAHS program. The secondary objective is to explore the features of green tourism in Japan. First, the historic development and current state of green tourism in Japan is reviewed. The case in study is a typical green tourism project concerning an organization of farmers in the Noto Peninsula—the Shunran-no-Sato group. The question of how to develop green tourism in the context of the GIAHS project and considering the sustainable development of rural society and its farming systems by increasing incomes of rural households, is investigated. The study combined literature review and in-depth interviews with farm inn owners to investigate tourism development in the depopulated rural areas of Japan, examine its challenges, and present this information to international readers.