Namisindwa District is bordered by Bududa District to the north, Kenya to the east and south, Tororo District to the south-west, and Manafwa District to the west. The district headquarters at Bupoto are located approximately 40 kilometres (25 mi), by road, south-east of Mbale, the largest city of in the sub-region.

Coordinates: 00°49′N 34°23′E