Nearly 50% of graduate students report experiencing emotional or psychological distress during their enrollment in graduate school. Levels of distress are particularly high for transgender and nonbinary graduate students who experience daily discrimination and marginalization. Universities and colleges have yet to address and accommodate the needs and experiences of transgender and nonbinary graduate students. Given the multitude of challenges these students may face, educational settings should not present additional barriers to educational success and well-being. In an effort to improve graduate education for transgender and nonbinary students, we add to the existing scholarship on affirming work with transgender undergraduate students by addressing the unique concerns of graduate students. We use a social-ecological model to identify sources of discrimination in post-secondary education and to provide transgender- and nonbinary-affirming recommendations at structural, interpersonal, and individual levels. For practitioners who wish to do personal work, we provide guidance for multicultural identity exploration. A table of recommendations and discussion of ways to implement our recommendations are provided.