This article aims to investigate the role and limitations of Track Two diplomacy in the development of regionalism in East Asia focusing on the case of the Network of East Asian Think-Tanks(NEAT). NEAT which was established as a result of East Asian regionalism has developed into one of the key Track Two mechanisms in the region. The development of NEAT with the structural linkage with Track One has not been free from the vicissitudes of East Asian regionalism based on ASEAN Plus Three (APT). East Asian regionalism once appeared as vision for the regional community through functional cooperation in various fields is stumbled by mushrooming regional architectures and the increasing rivalry among the powers. This study identifies the characteristics of NEAT by reviewing major issues with comparison to selected Track Two cases. The article argues that for the further development, NEAT needs to tackle the dilemma of autonomy referring a situation in which NEAT as a Track Two diplomacy has to seek autonomy and financial support from Track One simultaneously.