The modern-day international boundary between South Sudan and Uganda has its origins as a colonial administrative line separating Anglo–Egyptian Sudan from the Uganda Protectorate, both colonies then managed by the United Kingdom. Today, it runs from the tripoint with Kenya in the east for approximately 500 km to the tripoint with the Democratic Republic of the Congo in the west. It was initially delimited by a 1914 British Order describing the territory of the Uganda Protectorate. After independence, Uganda unilaterally established its own delimitation in its Constitution, first in 1967, and most recently in 1995.

There are several locations on the boundary that were originally described in vague terms, which have led to at least two areas of boundary disputes between South Sudan and Uganda. The first, near the South Sudanese town of Kajo Keji, is an area of contentious sovereignty with a de facto, ill-defined frontier following historic tribal boundaries. For the second, over a larger swath of territory near the South Sudanese town of Pajok, South Sudan and Uganda have explicit opposing claim lines. While there are occasional skirmishes directly related to the unresolved boundary questions, there are much broader problems of instability and conflict, especially in South Sudan due to its civil war. Lack of government control, problems with refugees, and general lawlessness in border regions have made demarcation and formalization of the international boundary between South Sudan and Uganda almost impossible.