JCIE served as the Japanese secretariat for the Korea-Japan Joint Committee for Promoting History Studies, an initiative agreed upon at a 1997 summit between Japanese Prime Minister Ryutaro Hashimoto and Korean President Kim Young-Sam. The Committee was launched in July 1997 with the goal of finding effective ways to enhance studies of history in the two countries. Each government appointed three members to jointly form an independent committee. The Joint Committee met fives times over the course of its work and commissioned joint research by scholars on ways to facilitate more active research on the history between the two countries. The final report of the Commission was finalized in the spring of 2000 and was submitted to both governments in May 2000.

In addition, as part of the work of the Committee, the Korea-Japan History Forum was held twice to incorporate a broader range of expertise and perspectives. Following the initial forum in Miyazaki in 1998, the second forum was held on September 10–13, 1999, in Taejon, Korea. In addition to the Committee members, 24 experts from both countries were invited to participate. The discussions centered on three topics: Korea-Japan relations in the post–World War II period; studies on Korea, Japan, and their relations in the postwar period; and intellectual exchanges between the two countries in the postwar period.