Military regimes favoring Islamic-oriented governments have dominated national politics since independence from Anglo-Egyptian co-rule in 1956. Sudan was embroiled in two prolonged civil wars during most of the remainder of the 20th century. These conflicts were rooted in northern economic, political, and social domination of largely non-Muslim, non-Arab southern Sudanese. The first civil war ended in 1972 but another broke out in 1983. Peace talks gained momentum in 2002-04 with the signing of several accords. The final North/South Comprehensive Peace Agreement (CPA), signed in January 2005, granted the southern rebels autonomy for six years followed by a referendum on independence for Southern Sudan. The referendum was held in January 2011 and indicated overwhelming support for independence. South Sudan became independent on 9 July 2011. Sudan and South Sudan have yet to fully implement security and economic agreements signed in September 2012 relating to the normalization of relations between the two countries. The final disposition of the contested Abyei region has also to be decided.

Following South Sudan's independence, conflict broke out between the government and the Sudan People's Liberation Movement-North in Southern Kordofan and Blue Nile states (together known as the Two Areas), and has resulted in 1.1 million internally displaced persons or severely affected persons needing humanitarian assistance. A separate conflict broke out in the western region of Darfur in 2003, displacing nearly 2 million people and causing thousands of deaths. Fighting in both the Two Areas and Darfur between government forces and opposition has largely subsided, however the civilian populations are affected by low-level violence including inter-tribal conflict and banditry, largely a result of weak rule of law. The UN and the African Union have jointly commanded a Darfur peacekeeping operation (UNAMID) since 2007. Peacekeeping troops have struggled to address insecurity in Darfur and have increasingly become targets for attacks by armed groups. Sudan also has faced refugee influxes from neighboring countries, primarily Ethiopia, Eritrea, Chad, Central African Republic, and South Sudan. Armed conflict, poor transport infrastructure, and denial of access by both the government and armed opposition have impeded the provision of humanitarian assistance to affected populations.