Its describers found it to be most similar to Scaphognathus among pterosaurs, albeit substantially larger (estimated skull length of 280-300 mm (11-12 in), estimated wingspan of at least 2.5 m (8.2 ft)). Because of the similarity, Harpactognathus was assigned to the subfamily Scaphognathinae of the family Rhamphorhynchidae. This genus is also notable for having a low bony crest running all the way to the tip of the beak (pterosaur bone crests usually do not reach the tip) and for being the oldest known Morrison Formation pterosaur, having been found in the Salt Wash Member (Kimmeridgian).