Objective: Participatory research has proven an effective method for improving health equity among American Indians/Alaska Natives (AI/ANs) by addressing power imbalances between communities and researchers, incorporating community knowledge and theory, ensuring mutual benefit and improving community capacity and programme sustainability. However, few studies have examined the implementation of these methods with urban Indian (UI) communities, a growing population currently comprising 71% of AI/ ANs. This paper describes the experiences of two academic researchers (one a Native doctoral student and another a White assistant professor) who sought to engage in participatory research with an UI community in Maryland. Method: The methodology employed was a literature review of Indigenous participatory research methods that aimed to inform the work of a youth-led project, and a reflexive case-study analysis. Results: Researchers discuss the social, structural and political inequalities that challenged their ability to engage in this process and identify three lessons learned associated with conducting participatory research with this population: logistics and recruitment, identifying the constraints and/or competing priorities of the community, and the importance of reflexivity and communication throughout the process. In an epilogue, the researchers highlight and reflect upon how they have since applied these lessons to strengthen their relationship with the community, yielding new and mutually beneficial participatory research projects. Conclusion: The findings presented advance research on participatory methodologies with UI communities and call for increased economic and political support of and long-term commitment to UI organisations to address the structural inequalities underpinning existing health inequities.