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International research indicates that sexual and gender minority students (including those who identify as LGBT) report lowered achievement relative to other students. Factors identified for this include the impact of increased victimization and less school belonging. However, supportive schooling structures and caregiver support have been shown in some instances to support their achievement. Presently there is little understanding of the specific factors associated with gender minority student achievement, despite the fact that such students often face additional and extreme challenges. This study addresses these issues and presents a local perspective on the topic. We used a nationally representative sample of secondary school students from the Youth 2000 Youth '12 survey to identify specific factors that support achievement for sexual minority (n = 485), gender minority (n = 298), and heterosexual cisgender (where one’s sex assigned at birth “matches” a binary gender identity, i.e., a male assigned at birth identifies as a boy/man, n = 7,064) students in New Zealand. We indicate that improving achievement for these students requires going beyond bullying prevention, to explore how student belonging and teacher expectations can be enhanced. Important implications for inclusive education are identified.