We address the emerging challenge of school segregation within the context of free school choice systems. Households take into account both proximity and demographic composition when deciding on which schools to send their children to, potentially exacerbating residential segregation. This raises an important question: can we strategically intervene in transportation networks to enhance school access and mitigate segregation? In this paper, we propose a novel, network agent-based model to explore this question. Through simulations in both synthetic and real-world networks, we demonstrate that enhancing school accessibility via transportation network interventions can lead to a reduction in school segregation, under specific conditions. We introduce group-based network centrality measures and show that increasing the centrality of certain neighborhood nodes with respect to a transportation network can be an effective strategy for strategic interventions. We conduct experiments in two synthetic network environments, as well as in an environment based on real-world data from Amsterdam, the Netherlands. In both cases, we simulate a population of representative agents emulating real citizens’ schooling preferences, and we assume that agents belong to two different groups (e.g., based on migration background). We show that, under specific homophily regimes in the population, school segregation can be reduced by up to 35%. Our proposed framework provides the foundation to explore how citizens’ preferences, school capacity, and public transportation can shape patterns of urban segregation.