The history of South Sudan comprises the history of the territory of present-day South Sudan and the peoples inhabiting the region.

South Sudan seceded from the Republic of Sudan in 2011. Geographically, South Sudan is not part of the Sudan region at all (the Sahel), forming as it does part of Sub-Saharan Africa. In modern terminology, it does, however, include parts of the East Sudanian Savanna. Its inclusion in "Sudan" is due to the southward expansion of the Ottoman Khedivate of Egypt in the 19th century, and its consequent inclusion in Mahdist Sudan, Anglo-Egyptian Sudan and the Republic of Sudan during 1885 to 2011.

South Sudan is mostly inhabited by Nilo-Saharan speaking peoples, with Niger-Congo speaking minorities. Historically, what is now South Sudan was dominated by Central Sudanic speaking peoples, but the presence of Nilotic peoples can be assumed from prehistoric times as well. Since about the 14th century, following the collapse of the Christian Nubian kingdoms of Makuria and Alodia, the Nilotic peoples gradually came to dominate the region.