The park's varied habitats support 68 mammal species. Rarities include impala, which, in Uganda, only lives in Lake Mburo, and Burchell’s zebra and eland which are found only here and in Kidepo.
Other species include warthog, buffalo, oribi, Defassa waterbuck and reedbuck. Leopard and hyena are also present while crocodile and over 300 hippos are found in the lake. Previously extinct in the park, lions have recently been sighted again.
Around 350 bird species have been recorded to date. These include the Red-faced Barbet, only seen in Lake Mburo, the endemic African Finfoot and the rare Shoebill. Other key species are the Papyrus Yellow Warbler, Saddle-billed Stork, Brown-chested Lapwing, African-wattled Lapwing, Carruther’s Cisticola, Tabora (Long-tailed) Cisticola, African Scops Owl, Abyssinian Ground Hornbill and White-winged Warbler.
Acacia woodland bird species are especially well represented, while forest species may be found in Rubanga forest. These include Blue-breasted Kingfisher, Hairy-breasted Barbet and Yellow-rumped Tinkerbird, among others.