This paper explores the possibilities and challenges for ethno-religious reconciliation through secondary school education in post-war Sri Lanka, with a specific focus on the Muslim and Tamil communities in the Northern city of Jaffna. In doing so, we position our paper within the growing field of 'education, conflict and emergencies' of which there has been a growing body of literature discussing this contentious relationship. The paper draws from an interdisciplinary and critical theoretical framework that aims to analyse the role of education for peacebuilding, through a multi-scalar application of four interconnected dimensions of social justice: redistribution, recognition, representation and reconciliation (or 4 R's, Novelli, Lopes Cardozo and Smith, 2015). We apply this framework to interpret primary data collected through an ethnographic study of two under-studied communities that have been disproportionately affected by the 1983 to 2009 civil war and displacement: the Northern Sri Lankan Muslims and Northern Sri Lankan Tamils. We find that structural inequalities in society are replicated in formal secondary school education and are perceived to be perpetuating ethno-religious conflict between Muslim and Tamil; second, through a multi-scalar analysis, formal peace education is perceived by respondents not to be meeting the needs of communities; and third, we observe how in response to failings of state peace education, an 'unofficial' Tamil-Muslim community education incorporating a social justice-based approach has emerged. This has facilitated a process of cross-community reconciliation between Muslim and Tamil through individual (teachers, students) and community (Muslim-Tamil community based organisations) agency. The paper concludes by offering suggestions for peace education policy and future research.