Unlike the great majority of crocodyliforms, its shin was longer than its thigh, suggesting it had some running ability.

[1] Fiorelli and Calvo ran a phylogenetic analysis of their new genus and found it to be allied with Shantungosuchus, Sichuanosuchus, Zosuchus, and Fruitachampsa.

This phylogeny complicated the paleobiogeographical history basal non-neosuchian crocodyliforms more derived than Protosuchia because Neuquensuchus is endemic to South America and other putative allied genera are older and from Laurasia.

[1] While several subsequent cladistic analyses recovered Neuquensuchus as a member of the notosuchian clade Ziphosuchia, a position which is more consistent with the fossil record and paleobiogeography of non-neosuchian mesoeucrocodylians,[2][3] the original position was upheld by an analysis conducted by Gabriel Liu and colleagues in 2017.

Neuquensuchus, a small, slender crocodyliform, had limb proportions well-suited to running, and was probably a swift, land-living animal.