This article reviews the history of environmental education research (EER) in Japan, casting a critical view on its fragmented nature, and proposes a future agenda for its development. Pollution (kogai) education research (KER) and nature conservation education research were initiated and developed by people from different backgrounds in the 1960s and 70s, which was followed by “EE” research in the 1970s. The establishment of the Japanese Society of Environmental Education (JSOEE) in 1990 could have linked them up under the banner of EE, yet KE was rather neglected within the JSOEE in the 1990s and 2000s, unlike nature conservation education. This is possibly because many key KE researchers did not join nor become active members of JSOEE, and the then Environmental Agency downplayed KE in the formulation of its EE policy. This KER-EER disconnect may account for the weak critical and social scientific perspectives in JSOEE and a “technocratic rationality” prevailing among its members who tend to regard EE as an instrument to achieve policy objectives. Existing studies also show other disconnects embedded in JSOEE—between research in Japan and abroad and between research in the present and the past, the former hardly drawing on the latter in each case. These disconnects may be due to the emphasis on a street-level pragmatism and a lack of theoretical discussion within JSOEE. After pointing out several features of Japanese EER in the 2010s, this article concludes by suggesting several agendas to address the patchwork condition and existing disconnects for the future of EER in Japan.