Over 200 species of invertebrates breed in the park, and many others overwinter here or use it as a stopping off point to rest and feed on their migration routes. Birds are the largest and most important group, so Monfragüe has been declared a Special Protection Area for Birds. The park is home to the largest breeding colony of black vultures, the Iberian imperial eagle and also has one of the largest concentrations of black stork nesting grounds.

Mammals include the Iberian lynx and the large population of deer and boar; among the reptiles, we find the ocellated lizard, and among the amphibians, the common salamander, the Iberian newt and the sharp-ribbed salamander.