For the past 50 years, agricultural research has contributed significantly to improving agricultural productivity for global food and nutrition security. The CGIAR, formerly the Consultative Group for International Agricultural Research, has been at the center of this effort. Accordingly, the orientation of CGIAR activities have profoundly changed over time from crop productivity improvement to broadened agendas, such as biodiversity conservation, environmental protection, and policy-related efforts. In parallel with the evolution of research orientation, the CGIAR also underwent operational reorganization. As the global food systems become more and more interconnected, and with global concerns about agriculture’s contribution to overstepping the planetary boundaries and driving climate crises, the CGIAR has tried to consolidate operations among the CGIAR Research Centers to address research needs of smallholder farmers in the 21st century. This review contextualizes the evolving role of the CGIAR vis-à-vis global challenges with reference to some highlights of Japan’s contribution in each of the following periods: the 1970s; the 1980s-1990s; the 2000s-2010s; and onwards. This exercise can contribute to understanding the drivers affecting the global food systems in retrospective and subsequently deriving foresights for future directions of the food system transformation.