Upper secondary education shapes gender segregation in higher education and the labor market. This study shows gendered elective course enrollment patterns in Chilean upper secondary education across seven subjects, examines their consistency across socioeconomic contexts, and identifies school-level moderators. Using national administrative data from 2012–2021 and multilevel models, we find that students make gender-stereotypical choices regardless of their prior achievement. Notably, in higher-socioeconomic-status schools, gender differences in enrollment are larger, suggesting that socioeconomic context amplifies gendered choices. Additionally, the gender culture of schools moderates segregation in field-of-study choices, indicating that the school environment plays an important role in shaping students’ educational trajectories. These findings highlight the need for targeted policies to address gender and socioeconomic disparities in education.