It is known from a partial holotype skull from the middle Stubensandstein (a deposit that dates back to the Norian stage and is part of the Löwenstein Formation) in Baden-Württemberg.

A. orbitoangulatus was first described by German paleontologist Friedrich von Huene in 1932,[1] who considered it a species of the theropod dinosaur Halticosaurus.

[2] A phylogenetic analysis performed by Sues & Schoch (2013) found Apatosuchus to be the sister taxon of the clade formed by Batrachotomus and more derived loricatans.

This position was supported by two unambiguous synapomorphies: the presence of a ridge on the dorsal surface of squamosal along the edge of supratemporal fossa, and concaved rear portion of the nasals at the midline.

The data matrix of Sues & Schoch (2013), a list of characteristics that was used in the analysis, was based on that of Nesbitt (2011), one of the most extensive on archosaurs.