The Mayanja River is located in central Uganda. It starts from the hill, northeast of the town of Wakiso, in Wakiso District, central Uganda. It flows in a north-western direction to empty into river kafu, Nakeseke district as it borders with Masindi district and Kyankwanzi district.

The source of river Mayanja is located in wakiso. River Mayanja enters river kafu near the village of Ndede, in Nakeseke district,

On its course north-westwards, the river traverses or forms the borders of the following districts: wakiso District, Mpigi district, kiboga district, kyankwanzi district and Nakeseke district. At its source, the altitude is approximately 1,140 meters (3,740 ft). At its point of entry into river kafu, the altitude is approximately 1,000 meters (3,300 ft). The length of river Mayanja, is approximately 150 kilometers (93 mi) from source to end.