In recent years, the U.S. Veterans Health Administration (VHA) has seen an increasing population of transgender and gender diverse (TGD) veterans accessing care. Approximately 139 per 100,000 VHA users had a gender identity disorder diagnosis documented in 2018 compared to 32.9 per 100,000 in 2013. Despite TGD patients being overrepresented within VHA, TGD veterans may distrust or face unique barriers with various aspects of the VHA, including health services research. Existing VHA health research focused on TGD populations is largely limited to secondary analyses of electronic health record data. Identifying strategies to enhance primary data collection is crucial for more deeply investigating health care challenges experienced by TGD veterans using VHA care. Additionally, describing health topics of importance for TGD veterans is important for making the research agenda more patient-centered. In this study, we offer veterans’ recommendations for researchers working with underrepresented populations based on our findings.