In 1962 at Independence, Kanungu District existed as one of the Counties of the former Kigezi (then called Kinkizi County). 

In 1974, when Rukungiri District was created it became part of Rukungiri District.

In July 2001, it achieved district Status, it comprised of 18 sub-counties and 9 town councils; Kanungu, Butogota, Kambuga and Kihihi Town Councils with 66 Parishes and 16 wards, and 520 villages.

Kanungu district lied in the fringes of the western rift valley with the Northern part forms part of the Rift valley with undulating plains with the middle part (sub-counties of Rugyeyo, Kirima and parts of Kanyantorogo) comprising of flat toped hills with gentle sloping sides and broad valleys. 

These hills gradually increase in height to the highlands of Rutenga with Burimbi peak of Mafuga being the highest at 82222ft (2503m) above sea level with some parts of Kihihi Sub County lying in the fringes of the western Eastern African rift valley.