The Rukarara rises in forested country in southern Rwanda to the east of the Congo-Nile Divide.

[1] The Kamiranzovu Swamp in the Nyungwe Forest Reserve provides a natural reservoir for the Rukarara.

The origin of the Nile, the furthest source from its mouth, is at an elevation of 7,966 feet (2,428 m), at latitude and longitude 2°16′055.962″S 29°19′052.470″E / 2.28221167°S 29.33124167°E / -2.28221167; 29.33124167.

The Nyirabugoyi and Rubyiro rivers are its main headwaters, both rising in the Nyungwe National Park.

[6] The Rukarara flows south and then east, emptying into the Mwogo River.