British explorer Samuel BAKER established the colony of Equatoria in 1870, in the name of the Ottoman Khedive of Egypt who claimed the territory. Headquartered in Gondokoro (near modern day Juba), Equatoria in theory composed most of what is now South Sudan. After being cut off from colonial administration during the Mahdist War from 1885-1898, Equatoria was made a state under the Anglo-Egyptian condominium in 1899. It was largely left to itself over the following decades, but Christian missionaries converted much of the population and facilitated the spread of English, rather than Arabic. Equatoria was ruled by British colonial administrators separately from what is now Sudan until the two colonies were combined at the 1947 Juba Conference, as part of British plans to prepare the region for independence. When Sudan gained its independence in 1956, it was with the understanding that the southerners would be able to participate fully in the political system. When the Arab Khartoum government reneged on its promises, a mutiny began that led to two prolonged periods of conflict (1955-1972 and 1983-2005) in which perhaps 2.5 million people died - mostly civilians - due to starvation and drought. Ongoing peace talks finally resulted in a Comprehensive Peace Agreement, signed in January 2005. As part of this agreement, the south was granted a six-year period of autonomy to be followed by a referendum on final status. The result of this referendum, held in January 2011, was a vote of 98% in favor of secession.

Since independence on 9 July 2011, South Sudan has struggled with good governance and nation building and has attempted to control opposition forces operating in its territory. Economic conditions have deteriorated since January 2012 when the government decided to shut down oil production following bilateral disagreements with Sudan. In December 2013, conflict between government and opposition forces killed tens of thousands and led to a dire humanitarian crisis with millions of South Sudanese displaced and food insecure. The warring parties signed a peace agreement in August 2015 that created a transitional government of national unity in April 2016. However, in July 2016, fighting broke out in Juba between the two principal signatories, plunging the country back into conflict. A "revitalized" peace agreement signed in September 2018 is currently in the process of being implemented.