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Background: Adolescents facing gender-based violence (GBV) experience layered risks shaped by intersecting identities such as disability, sexuality, and class. While schools are key sites for prevention, intervention impact remains uneven, and intersectionality is often overlooked. Aim: This integrative review examines how school-based GBV prevention programs engage with intersectionality, identifying structural gaps and equity-promoting practices for marginalised adolescents. Methodology: A systematic search across PubMed, PsycINFO, ERIC, and Web of Science identified 15 evaluative studies, appraised using the JBI framework and synthesised through deductive content analysis with an intersectionality-informed matrix. Results: Many programs improved awareness and peer dynamics, yet marginalised adolescents were often underserved. Intersectional inclusion was rarely embedded in design, with most adaptations emerging reactively. Programs with participatory and context-responsive elements showed greater promise but lacked structural anchoring. Conclusions: To achieve transformative and equitable school-based GBV prevention, intersectionality must be embedded not only as an analytical lens but as a guiding principle for program design, implementation, and evaluation. Lasting impact requires structural integration, rights-based frameworks, and institutional commitment that centres the voices and agency of marginalised adolescents.