We highlight the historical and contemporary policies that govern paleontological research on federally recognized Native American lands. The United States has a long history of fossil dispossession from Indigenous Peoples, and federal policies surrounding the management of Native American lands (i.e., reservations), and the geological resources therein, have changed through time. These changes reflect shifting popular and political ideologies regarding Native American nations’ sovereignty and self-governance. As of 2022, the United States has a government-to-government relationship with federally recognized Tribal entities, but that has not always been the case. Historians have divided post-contact Native American federal policy into distinct eras: Colonial Times to 1820, Native American Removal and Reservation (1820–1887), Allotments and Attempted Assimilation (1887–1934), Reorganization and Preservation (1934–1953), Termination and Relocation (1953–1968), and Tribal Self-Determination (1968–present). Documentation of how the federal policies from each of these eras continue to impact current paleontological research is limited. We summarize major legislative actions, court cases, and historical events that have affected paleontological resource management in Native American territory. We use this historical context to identify federal policy gaps and highlight legal nuances associated with fossil collection and ownership, particularly given the importance of fossils to some Native Americans’ cultural patrimony. Finally, we explore how these gaps affect scientific research and highlight best practices for conducting paleontological research on vertebrate, invertebrate, and paleobotanical body and trace fossils using the CARE (Collective Benefit, Authority to Control, Responsibility, Ethics) Principles for Indigenous Data Governance (https://www.gida-global.org/care).