Known as "terror birds", these lived in what is now Argentina during the Early and Middle Miocene; the Santa Cruz Formation in Patagonia contains numerous specimens.

[3][7] They also named Palaeociconia cristata based on 2 vertebrae and 2 ungues from Santa Cruz, believing that they were from a fossil stork related to Ciconia.

[9][7][4] In August 1891, Ameghino named Tolmodus inflatus based on a fragment of the right premaxilla that had been collected by Carlos in the same middle Miocene deposits in Santa Cruz.

[10][4] Ameghino originally considered the taxon an edentate mammal related to Phorusrhacos, but 2 months later in June he synonymized the two and realized that they were actually flightless carnivorous birds, a conclusion made earlier by Moreno.

[11][4] By the end of the "Argentine Bone Wars", many Patagornis fossils had been collected and majority reside in the Museo de la Plata or the Natural History Museum, London.

[14][4][15] The Museo de la Plata also collected a nearly complete Patagornis skeleton, including a skull, though it is poorly preserved.

[18][12] The ungual phalanges preserved in Patagornis and its distant relative Mesembriornis are large, curved, and thin laterally, likely being used to stab prey based on those of modern predatory birds.

[19] Due to the great preservation of Patagornis and its relatives, comparisons with other taxa and detailed classification are much easier compared to other phorusrhacids.

In 2003 during their redescription of phorusrhacidae, Herculano Alvarenga and Elizabeth Hofling created a new subfamily, Patagornithinae, with Patagornis as the type genus.

[18] The following phylogenetic tree shows the internal relationships of Phorusrhacidae under the exclusion of Brontornis as published by Degrange and colleagues in 2015, which recovers Patagornis as a member of a large clade that includes Physornis, Phorusrhacos and Andalgalornis, among others.

[21] Patagornis is also known from the coastal Monte Leon Formation that was in the same region in Santa Cruz, but part of the older lower Miocene age.