There is an urgent need to explore the complex experiences of high school student-athletes, especially considering the growing investment in youth sports and its implications on students’ mental health and identity development. This mixed-methods research study delves into the effects of intersectionality on high school student-athletes’ sense of belonging within a coeducational Catholic high school environment. Through quantitative analysis utilizing the Psychological Sense of School Membership scale (Goodenow, 1993), complemented by a Confirmatory Factor Analysis (CFA) to affirm the scale’s structure, and qualitative insights gathered from focus groups, the nuanced ways in which intersecting identities impact student-athlete belongingness and well-being are revealed. Key findings show that student-athletes perceive a strong sense of belonging within the school community, but face challenges in having to suppress parts of their identities to fit into the athlete role or to conform to school norms. Additionally, findings suggest a misalignment between the school’s mission and its practice with instances where individual identities are commodified, thus abandoning the holistic educational goals of the school. The intersection of race, gender, and sport identification emerged as a significant factor in creating varied experiences of belonging among student-athletes. Socioeconomic status and the pursuit of authentic relationships outside of their athletic performance were also identified as barriers to peer relationships, while meaningful connections with teachers were found to stem from a holistic approach to education. The study advocates for an educational environment that recognizes and supports the intersecting identities of student-athletes, proposing that such an approach is essential for promoting inclusive education and enhancing the experiences of all student-athletes.