The CGIAR, formerly the Consultative Group on International Agricultural Research, was established in 1971 to support investments in research and technology development geared toward increasing food production in the food-deficit countries of the world. Japan has cooperated with the CGIAR since becoming a member in 1972 and has made significant contributions in terms of both financial and human resources. In 2021, the CGIAR celebrates its 50th anniversary. This Special Issue brings together the contributions of Japan and Japanese researchers to sustainable food system transformation. It includes a review article on CGIAR’s international agricultural research and the role of Japan. There are 14 review papers from individual CGIAR Research Centers specialized in their respective fields, ranging from crops, livestock, forestry, fisheries, and natural resource management to policies, and an article from the Japan International Research Center for Agricultural Sciences (JIRCAS) that has long- term collaboration with the CGIAR. This introductory paper will briefly provide the background and rationale for this Special Issue and a short introduction of the papers presented herein.