International non-governmental organizations (INGOs) have played a critical role in peace building by engaging mostly in humanitarian aid but are faced with a vast number of challenges. In the case of Kenya-South Sudan, INGOs have been critical in the humanitarian aid especially in refugee camps. This research was motivated by the need for empirical data and evidence in the challenges these INGOs face in achieving peace along the Kenya South Sudan border through track three diplomacy. The study problem was the challenges INGOs face in peace building along the Kenya South Sudan border through Track Three diplomacy. The overall objective was to examine the challenges INGOs face in peace building efforts along the Kenya South Sudan border using track three diplomacy. The specific objectives were to examine the challenges of INGOs in peace building through track three diplomacy, through socio-economic activities and through political involvement along the Kenya South Sudan border. The study was anchored on complexity theoretical framework that guided the analysis of the challenges of international NGOs in peace building in Kenya-South Sudan border relations.