This paper presents the findings from a case study research comparing the impact on social cohesion of segregated and mixed schooling systems of Lebanese and Syrian refugee students. Based on qualitative research with students, their families and teachers, the paper argues that perceptions and relationships between students in mixed classes improve over time. Though this change bears little impact on relationships beyond the school or the attitudes and relationships of family and community members, it does equip students with the ability to counter prevailing prejudice. The adoption by ministries and partner donors of an integrated approach bridging educational reform with social cohesion programmes within the school will support improved social relationships as well as educational attainment for all school students. The paper makes several recommendations, including the need to: prioritise improvement in the quality of educational standards; acknowledge the positive impact of first-shift schooling; provide teachers in the afternoon shift with administrative, logistical and academic support; improve responsiveness to arising needs and issues; support school staff, particularly school administrators with skills and training on dealing with conflict; support extracurricular activities that bring together Lebanese students with Syrian student; and target girls of both first and second shifts in extracurricular activities that are culturally appropriate.