In this paper, we discuss a rapid-fire study involving Indigenous and non-Indigenous stakeholders from the urban Indigenous health sector who collaborated to produce an “Urban COVID-19 Systems Map.” The map outlines the behaviours, actions and responses that stakeholders identified as mitigating or exacerbating COVID-19 risks in urban Indigenous communities. Data were collected and analysed during the height of the pandemic in 2021. We begin by introducing the characteristics of system thinking—the methodology that informed our research—and consider its use in Indigenous health research more broadly. We then outline our utilisation of system thinking and discuss how it was applied to the three workshops. System thinking contributes to collaboration and collective debate amongst stakeholders and aims to produce holistic understandings of complex problems, such as pandemics. This article provides a reflective overview of the benefits and challenges of applying system thinking in Indigenous health research whilst also sharing some of the research findings. We argue that centralising the voices of stakeholders, particularly Indigenous stakeholders, is critical to developing and implementing effective and culturally appropriate responses to pandemics and is equally as important to the preparedness for future pandemics.