For decades, U.S. education policy has focused on the persistent achievement gap based on race and class in public schools. Within this test-based accountability context, math and reading achievement have been prioritized, and students have experienced inequitable access to rigorous science learning opportunities. Some scholars have drawn on cultural reproduction theory to examine the relationship between student background and achievement without accounting for the role of U.S. schools in structuring differential access to learning opportunities. This study aims to fill a gap in the literature by employing a critical quantitative lens and intersectional framework to examine how school structures, norms, and instructional practices contribute to stratification and systematic inequality in schools based on student background, shifting the focus from the achievement gap to the opportunity gap in U.S. schools. Using nationally representative U.S. data from PISA 2015, this dissertation employs latent class analysis (LCA) with auxiliary variables to examine the relationship between intersectional student background profiles, student sense of belonging, and student learning opportunities in science for 15-year-olds. A structural equation model (SEM) is used to extend these findings by examining potential mediators of intersectional student background and science achievement – opportunity to learn (OTL), sense of belonging, and student perceptions of academic climate – to account for inequitable learning environments in schools. Multilevel structural equation modeling (SEM) is then used to analyze science learning opportunities and academic press as mediators of intersectional student background and scientific literacy outcomes, as well as the school norms and structures that contribute to these experiences and outcomes. The findings from these studies revealed systemic inequality highlighted by a wealth gap between intersectional background groups of similar affluence based on parent occupational status and education. Further, gender disparities in OTL, sense of belonging to school, perceptions of academic climate, and scientific literacy outcomes consistently emerged across studies. Academic press was identified as an important mediator of student background and science achievement, and was a negative predictor of scientific literacy outcomes. Finally, while academic tracking predicted school mean academic press and OTL, school-level academic climate predicted school mean science achievement. However, there were significant differences in school-level academic climate between school contexts, pointing to a potential focal area to improve equity in schools. By identifying malleable school structures, norms, and instructional practices that shape students’ educational experiences and subsequent outcomes, this study provides potential policy levers for addressing concerns about equity in science education, including gaps in science opportunity to learn, engagement, achievement, and postsecondary outcomes.