[1] Its taxonomic position is highly controversial, with authors alternatively considering it to be a cariamiform, typically a phorusrhacid (terror bird) or an anserimorph.

If these conclusions are valid, this would mean that there are three groups of giant basal anseriformes, in chronological order of divergence: the gastornithids (Gastornis and kin), Brontornis, and finally the mihirungs of Australia.

The exact systematic assignment of Brontornis and the Brontornithidae is very uncertain and in a constant flux, which is largely due to the fragmentary nature of the remains.

[1] However, a Tibiotarsus of a large bird similar to Brontornis was found in Oligocene strata in Salla-Luribay, Bolivia, making it the oldest known Brontornithid fossil known.

These are related to the seriama, sharing features such as a hook-shaped upper beak and the curved ungues, which had sharp claws and thus distinguish the birds as predatory carnivores.

The allocation to the Phorusrhacidae was mainly based of the strong lower jaw symphysis and the targeted Tarsometatatarsus at the front and back, and was supported by Herculano M. F. Alvarenga and Elizabeth Höfling in 2003.

[1] A revision of the genre of Federico L. Agnolin in 2007 rejects the assignment based on these characteristics to the Phorusrhacids, since they also occur in other early large running birds, for example in Anserimorphs or within the Dromornithidae.

[6] The rotation of the middle shape of the Tibiotarsus and the construction of the square leg suggest for a closer relationship with the goose family (aneriform) rather than Phorusrhacidae.

[11][12][6] This phylogenetic position for Brontornis had originally been favored by the first descriptions of the genus, but Mathilde Dolgopol de Sáez classified it as a relative of geese and Gastornis in 1927.

[17] The lack of the striking bone footbridge (Pons Supratendineus) on the front of the lower joint of the tibiotarsus of Brontornis was also pointed out several times, which in occurs in the Phorusrhacidae.

A comparison of the tarsometatarsi of two B. burmeisteri specimens, FM-P13259 and MLP-91 (lectotype), both coming from the same geographical region and geological formation, shows them as not to present any anatomical differences, apart from size, where in the first is around one third smaller than the second.

[1] Correspondingly, art and skull reconstructions depicted Brontornis with a sharp and hooked top beak,[1] though paleontologists are unsure because the tip of the preserved mandibles is missing.

Likewise, the ungues of Brontornis do not show stronger bends compared to Phorusrhacids and thus do not allow raptor-like claws for tearing meat, which suggests a more plant-based diet.