The generic name is in honour of John Nyaphuli of the National Museum of Bloemfontein, who contributed extensively to South African palaeontology and discovered the holotype specimen of Nyaphulia in 1982.

Phylogenetic analyses since then consistently found "E." oelofseni to be more basal than the type species of Eodicynodon, rather than its sister taxon, which researchers suggested indicated it should belong to a distinct genus.

It was discovered on Botterkraal Farm in the Prince Albert District of Western Cape, South Africa in rocks from the lower Abrahamskraal Formation.

[1][2] This locality belongs to the Eodicynodon Assemblage Zone biozone, which has not been firmly dated but is roughly constrained to between 266.9 and 264.7 million years old during the Wordian stage of the middle Permian period (Guadalupian).

The skull has also been taphonomically distorted and damaged by compression during fossilisation, deforming portions of the snout, crushing the palate, and displacing the entire occiput up and to the side.

Consequently, they erected the new genus Nyaphulia for "E." oelofseni, named in honour of John Nyaphuli for his extensive work on South African palaeontology in the Karoo, including the discovery of NMQR 2913 itself.

However, unlike earlier anomodonts, both the premaxilla and the tip of the dentaries in the upper and lower jaws, respectively, are entirely toothless, suggesting Nyaphulia had a beak like other dicynodonts.

The palatal surface of the premaxillae extends back somewhat, however, it is short and the bony internal nostrils (choanae) still open near the front of the mouth at the level of the maxillary teeth.

[1][2] Rubidge (1990) originally referred Nyaphulia to the genus Eodicynodon on the basis of shared plesiomorphic (ancestrally present) characteristics that are also absent in any later dicynodonts.

Rubidge (1990) nonetheless recognised it at least as a distinct species ("E." oelofseni), primarily on the basis of the number and position of the maxillary teeth and the lack of canine tusks.

From their results, they argued that there was no compelling reason to believe they were each other's closest relatives and that E. oosthuizeni has much more in common with later dicynodonts, and therefore that "E." oelofseni likely represented a distinct taxon.

[9] This view has been supported by later researchers and upheld by further analyses, but a formal reassignment was avoided until it could be fully redescribed, accomplished by Duhamel and colleagues in 2024.

The following phylogeny is modified from one of the Bayesian phylogenetic analysis Duhamel et al. (2024):[1] Biseridens Anomocephalus Tiarajudens Otsheria Suminia Ulemica Patranomodon Galechirus Galeops Galepus Nyaphulia Eodicynodon Colobodectes Lanthanostegus Pylaecephalidae More derived dicynodonts Nyaphulia shares with other dicynodonts the absence of premaxillary teeth, forward-projecting transverse processes of the pterygoid with pterygoid keels, a lateral dentary shelf, and the absence of vertical lamina on the surangular of the lower jaw.

At the same time, it differs from Eodicynodon and all other dicynodonts by the combination of lacking a tusk and caniniform process, absence of a secondary palate, lateral exposure of the septomaxilla, and a parabasisphenoid that reaches the interpterygoid vacuity—all features it shares with various earlier anomodonts.

Other therapsids included the much larger herbivorous tapinocephalian Tapinocaninus as well as several large predators: the anteosaur Australosyodon, the scylacosaurid therocephalian Eutheriodon,[13] and a gorgonopsian of indeterminable affinity.