While literature on university governance in Canada has identified key challenges that need to be addressed, it largely overlooks calls for change towards indigenization within post-secondary institutions. Efforts towards indigenization are being made in practice, but little has been done to reflect on what this means for university governance specifically. This paper contributes to this gap in understanding by drawing upon experiences within Yukon College's transition to Yukon University. We identify three challenges that have emerged in the institution's approach to grappling with the intersection of university governance and indigenization, including questions related to who is driving the process, who represents Indigenous voices, who defines truth and knowledge, and how power dynamics can be shifted. We demonstrate how these challenges are playing out at Yukon University, how the institution is responding to them, and the broader issues they reveal. We also identify three opportunities that may be useful for other post-secondary institutions, including opportunities to move towards taking action, ensuring accountability, creating safe spaces, and addressing power dynamics. We hope to spark broader discussions and reflections from post-secondary institutions regarding the relationship between university governance and indigenization.