The Institute was originally founded in 1998 as the Institute of Canadian Studies under the leadership of Dr. Chad Gaffield. It housed the undergraduate and collaborative PhD programs in Canadian Studies. In 2004, Dr. Georges Sioui, professor of Religious Studies and Huron-Wendat scholar from Wendake, was hired to create and coordinate a new Aboriginal Studies program. The program was inaugurated at a special ceremony on 15 April 2004 at Algonquin Elder William Commanda’s Lodge, in Kitigan Zibi Algonquin Anishinaabe First Nation near Maniwaki. Thirty people gathered in the Lodge and participated in a Talking Circle ceremony officiated by Commanda saying how they, as “relatives of this child prepared it to be born” (as the metaphor is now set), would be involved in establishing  “the kind of care [it] needs to receive if it is to become the strong and happy offspring it was dreamed to become.” Dr. Sioui ran the program until his retirement, and remains an emeritus professor with the Institute.

Since 2010, the Institute has been home to the research lab and offices belonging to the Chair in Métis Research and, as interest in Indigenous Studies grew both at the University of Ottawa, the Institute of Canadian Studies was renamed the Institute of Canadian and Aboriginal Studies in January 2013. At the time, the faculty members who taught in the program either came from other departments or were cross-appointed to teach in the undergraduate Aboriginal Studies program. Two such cross-appointed professors remain central to the academic mission of the program—Dr. Sonia Wesche (Dept of Geography, Environment, and Geomatics) and Dr. Daniel Rück (Dept of History).

On 24 September 2014 the building housing the Institute of Canadian and Aboriginal Studies was redesignated as William Commanda Hall. The designation of the building was initiated by Dean of the Faculty of Arts, Antoni Lewkowicz, and undertaken in consultation with the family of the late Elder, William Commanda, including part-time professor and alumna, Claudette Commanda.

By 2017-18 it became clear that the University of Ottawa required a dedicated research and teaching institute for Indigenous scholars. uOttawa is uniquely placed to make important contributions to Indigenous Studies in both English and French due its location in the national capital region, a crossroads between English and French Canada. The process of establishing the new Institute included consultations with other faculties, Indigenous professors, the department chairs of the Faculty of Arts, the council of the Faculty of Social Sciences, students, and the Indigenous Education Council for the University. 

In 2019, the Institute of Canadian and Aboriginal Studies was officially renamed the Institute of Indigenous Research and Studies (IIRS), and the Aboriginal Studies program was transformed into the Department of Indigenous Studies within IIRS. This meant that, for the first time in uOttawa’s history, tenurable faculty members could be hired directly into IIRS, a monumental step toward establishing the ability of Indigenous peoples to begin shaping and transforming research and teaching in the IIRS. Dr. Brenda Macdougall (Metis / ahpitowkosisan) was named director in 2019 and two new Assistant Professors, Dr. Veldon Coburn (Algonquin) and Dr. Pierrot Ross-Tremblay (Innu), were hired. This was a critical step in ensuring that Indigenous scholars were determining the direction of this new Institute. The Institute is now home to both the Canada Research Chair in Indigenous Intellectual Traditions and Self-Determination, and the University Research Chair in Metis Family and Community Traditions, held by Dr. Ross-Tremblay and Dr. Macdougall respectively.

The foundation for this new direction for the Institute stems from the long-term work undertaken by Dr. Timothy J. Stanley during his tenure as Director of the former Institute of Canadian and Aboriginal Studies. Following his retirement, Dr. Stanley became an emeritus professor with the Institute.