In the last two decades of the war between the north and South Sudan, which ended with the signing of the Comprehensive Peace Agreement (CPA) in 2005, ethnic identities were manipulated leading to a second tier of wars involving southerners - ‘the south-south wars’. When the wars escalated, they added significantly to the cumulative death toll, with both victims and perpetrators being southerners. Despite the commission of widespread, grave crimes in the wars, justice was excluded in the CPA process through amnesty, with a view to facilitating the transition. This study explores the relevance of customary reconciliation in South Sudan for promoting Transitional Justice (‘TJ’) in the country. The study is premised on the need to achieve a balance between the imperative of TJ for the ‘south-south wars’ and the need for peace in the country. It argues that post-CPA conflicts are, to great extent, by-products of the legacies of the wars and as such, the same communities are the most affected. Based on the conceptual understandings of bottom-up TJ, the study utilizes ethnographical tools to explore the customary reconciliation practices of the Dinka, Nuer and Zande, the three largest groups in the country. The validity of the findings is enhanced by the use of triangulation and grounded theory. The primary finding is that in the absence of formal official interventions, customary reconciliation has the potential to promote bottom-up TJ as a tool for reparation, reintegration, truth telling, healing, etc. The study argues that a combination of modern methods and customary reconciliation could be utilized to mitigate the limitations of customary reconciliation. Towards enhancing TJ intervention, the study argues for an increased focus on cultural perspectives relevant to TJ as this could, among other benefits, mitigate the competing interests of peace and justice.