The foundation's founding chairman was former Shanghai mayor Wang Daohan, honorary chairman Rong Yiren. Negotiations with SEF stopped in 1999, and after Wang's death in 2005, no new chair was appointed until 2008. Following the election of Ma Ying-jeou to the presidency of Taiwan, talks between ARATS and SEF have restarted and progress was made in the areas of transport and economy such as the Three Links in 2008 and Economic Cooperation Framework Agreement in 2010. Chen Yunlin, who was formerly head of the Taiwan Affairs Office, was the head of ARATS from 2008 to 2013. He has met his counterpart Chiang Pin-kung in 2008.[4]
In 2024, Taiwan's Mainland Affairs Council banned its citizens from working at ARATS due to national security concerns.[5]