The diverse nature of Muotkatunturi Wilderness Reserve provides habitats for many bird species, and its remoteness guarantees a quiet environment for observing them. Species of the mires, fell uplands, treeless fells and coniferous forest zone are found here. Many fell species have strong populations in Muotkatunturi. They include the ptarmigan (Lagopus muta), Eurasian dotterel (Eudromias morinellus), bar-tailed godwit (Limosa lapponica), long-tailed jaeger (Stercorarius longicaudus) and snow bunting (Plectrophenax nivalis).

The most common birds in the Wilderness Reserve are the willow warbler (Phylloscopus trochilus), meadow pipit (Anthus pratensis) and brambling (Fringilla montifringilla). The Lapland longspur (Calcarius lapponicus), redwing (Turdus iliacus) and European golden plover (Pluvialis apricaria) also have large populations here. The long-tailed duck (Clangula hyemalis), dunlin (Calidris alpina), two-barred crossbill (Loxia leucoptera) and red-throated pipit (Anthus cervinus) are some of the rarer species in this area; they are not endangered or protected under EU directives, however.
The best time for birdwatching in Muotkatunturi Wilderness Reserve is early summer as migratory birds return there to nest.