The district lies between Huye and Rusizi in the south-west of Rwanda, and contains much of the former Gikongoro Province, which was disbanded in 2006. It also contains the eastern half of Nyungwe Forest, a popular tourist destination, being one of the last remaining forest areas of Rwanda and home to chimpanzees and many other species of primate.

Nyamagabe district is divided into 17 sectors (imirenge): Buruhukiro, Cyanika, Gatare, Kaduha, Kamegeli, Kibirizi, Kibumbwe, Kitabi, Mbazi, Mugano, Musange, Musebeya, Mushubi, Nkomane, Gasaka, Tare and Uwinkingi.