Indigenous health research in Canada has a chequered past and has been identified as problematic and lacking in appropriate collaboration with Indigenous people. The Tri-Council Policy Statement on Ethical Conduct for Research Involving Humans, Chapter 9 describes ethical conduct of research regarding First Nations, Inuit, and Métis Peoples. First Nations Ownership, Control, Access, and Possession (OCAP®) Principles highlight the necessity of Indigenous engagement and governance. To ensure that the aims and activities of the research being developed are in full and meaningful partnership with Indigenous peoples and communities, community-based participatory research (CBPR) methods provide a process in which full engagement is possible. Research utilizing secondary data sets, such as routinely collected health administrative data, should no longer be excluded from this approach. Our aim was to describe how our research team of academic researchers and a national Indigenous health organization adapted CBPR methods in a research project using previously collected data to examine end-of-life health care service delivery gaps for Indigenous people in Ontario. We describe the process of how we developed our research partnership and how grounding principles and Indigenous ways of knowing guided our work together. Through the adaptation of CBPR methods, our research partnership illustrates a process of engagement that can guide others hoping to conduct Indigenous health research using previously collected data. We also present a transparent research agreement negotiated equally by a national Indigenous health organization and research scientists, which can also be used as a framework for others wishing to establish similar research partnerships. Ensuring that Indigenous perspectives are central to and reflected in the research process is essential when using health administrative data.