The genus was named in 2002 by Stephen Czerkas and Ji Qiang. The type species is Pterorhynchus wellnhoferi. The genus name is derived from Greek pteron, "wing" and rhynchos, "snout", in reference to the tall crest on the head. The specific name honours the German pterosaur researcher Peter Wellnhofer. The describers assigned Pterorhynchus to the Rhamphorhynchidae. David Unwin's recent book The Pterosaurs: From Deep Time regarded it as a Cretaceous genus,[3] but this was based on old information. He also suggested that it was a scaphognathine, related to Scaphognathus.