In a national survey of more than 19,000 U.S. high school students, we compared how LGBTQ youth and their non-LGBTQ peers felt at school and how they perceived social and academic experiences. We examined differences in emotions and school experiences across gender identities, sexual identities, and their intersections. LGBTQ adolescents reported significantly more frequent negative emotions and bullying, consistent with previous research. LGBTQ students also reported less frequent experiences of positive emotions at school and less frequent positive school experiences (i.e., positive peer and teacher relationships, subjective task value, and persistence support). Students who were both gender and sexual identity minority reported the most frequent negative and least frequent positive experiences at school, compared to students who were neither a gender or sexual identity minority. Analyses of the intersection of gender and sexual identity showed that heterosexual male students experienced more frequent positive emotions and school experiences, and fewer negative emotions and bullying, compared to all other groups. We discuss how these differences might be addressed through school interventions and future research.