This research seeks to extend current understandings of the experiences and challenges that face refugee students learning in protracted refugee situations like Jordan. The project looks at Syrian refugee students’ experiences and perceptions of learning in Jordan’s segregated, double-shift schools. Education for refugee has focused on enhancing access and learning quality, seeking to allow refugee children to gain a sense of normalcy and create opportunities for their futures. However, little attention has been paid to how refugee students’ experience their learning spaces in more long-term refugee situations, and how their well-being, aspirations, and perceptions of self and the future are influenced by the education initiatives that refugee-hosting nations put forth. Through a qualitative phenomenological approach, I draw on Sen’s Capability Approach to explore children’s perceptions of their well-being and experiences in schools and outside schools. I engage with students to understand the values and hopes that children have for their present and future, and I examine how these values are shaped by the interactions between schools and the social, economic, and political factors that affect students. This study uses visual-based methods with children to elicit conversations, and also draws on five teacher interviews and classroom observations. The findings of this study portray the important role that schools play in influencing how refugee children’s identities are shaped, and the extent to which students’ school reinforce or transform the limitations that refugee children experience within their hosting nation. It contributes to understanding the values that children believe are important for their well-being in these schools, and provides a discussion on how children’s needs and the challenges they face can also vary across age and gender. The research offers compelling insight into how negative practices within schools, how segregated school structures, and a lack of alignment between policymaking and practice can harm children’s development and undermine the benefits of access to education. These findings illustrate the importance of situating refugee students’ well-being in relation to their social, political, economic, and cultural factors. Finally, the study also calls for a greater understanding of how the well-being of parents and teachers can influence refugee students’ own well-being.