This article investigates educational experiences of transgender and gender non-conforming (TGNC) youth living in Northern Ireland (NI) through a mixed-methods research design and analytical framework of heteronormativity. It draws on large-scale survey data which, for the first time in NI, captured the experiences of 16 year olds who identify as TGNC. This provides a baseline for the demographics of TGNC youth living in NI and the levels of homophobic and transphobic abuse they experience in school. Survey data are triangulated with findings from five qualitative interviews exploring the subjective experiences of TGNC youth in educational environments. Interview data reveal how heteronormativity is embedded in educational policies and practices. This institutionalisation of heteronormativity was found to be linked to the influence of conservative Christian values, which inhibit open and positive dialogue about TGNC and non-heterosexual identities, in educational domains. We show how educational environments shaped by heteronormativity and conservative Christian values serve to undermine the self-determination and freedom of expression of TGNC youth. In conclusion, we offer practical examples of counter-heteronormative interventions that will assist educators and schools in NI to develop empathetic practice and supportive environments that will erode the inequality and injustice TGNC youth experience in pedagogical institutions.