During Southern Sudan’s second period of civil war, non-governmental organizations (NGOs) provided almost all of the region’s public services and greatly influenced local administration. Refugee movements, inadequate infrastructures, food shortages, accountability issues, disputes and other difficulties overwhelmed both the agencies and newly developed civil authorities. Blurred distinctions between political and humanitarian activities resulted, as demonstrated in a controversy surrounding a 2004 distribution of relief food in Central Equatoria State. Based on analysis of documents, correspondence and interviews, this case study of Kajo Keji reveals many of the challenges posed by NGO activity in Southern Sudan and other countries emerging from long-term instability. Given recurrent criticisms of NGOs in war-torn areas of Africa, agency operations must be appropriately geared to affected populations and scrutinized by governments, donors, recipients and the media.