This paper develops and applies the emergent concept of institutional transphobia to explore the barriers to transgender research in early years education. It argues that institutional processes embed and disguise the logic of transphobia by drawing on dominant, taken-for-granted claims of the inappropriateness or irrelevance of gender-focused education interventions that challenge cis-normativity and heteronormativity. Drawing on the barriers and difficulties experienced through a PhD journey, the paper explores how institutional transphobia was evident in the seemingly neutral reasons for denying site access and ethics approvals, divergent institutional ethics requirements, the tensions between individual support and institutional processes, and the expectations on research higher degree students. The paper concludes that current processes and priorities must be challenged and replaced with an institutional mandate that explicitly values and welcomes transgender research as a priority.