The Queensland Aboriginal and Islander Health Council (QAIHC) lead and govern the Centre for Clinical Research Excellence (CCRE), which has a focus on circulatory and associated conditions in urban Aboriginal and Torres Strait Islander communities. The CCRE is a partnership between QAIHC and Monash University, the Queensland University of Technology, the University of Queensland, James Cook University, the National Heart Foundation, and the University of Wollongong. The establishment of the CCRE under the community-controlled model of governance is unique and presents both opportunities and challenges for innovative partnerships between universities and Aboriginal and Torres Strait Islander community organisations. This paper outlines the processes and strategies used to establish a multi-institutional research centre that is governed by the Aboriginal and Torres Strait Islander community-controlled health sector.