Germanodactylus is described as being "raven-sized" in weight. G. cristatus had a 0.98 wingspan (3.2 ft) and a 13 centimeter long (5.1 in) skull, while G. rhamphastinus was somewhat larger, with a 1.08 meter wingspan (3.5 ft) and a skull 21 centimeters long (8.3 in).
Germanodactylus is known for its head crest, which had a bony portion (a low ridge running up the midline of the skull) and a soft-tissue portion that more than doubled its height. The bony part does not go as far up the head in G. cristatus as in G. rhamphastinus. The soft-tissue portion was not known early on, being first described in 2002 by S. Christopher Bennett. It was probably composed of cornified epidermis. Germanodactylus is the first genus for which a soft-tissue component of the crest is known, but similar structures were probably widespread among pterosaurs.
This genus is unspecialized compared to the pterosaurs of the Cretaceous, and has had varying placements in Pterosauria. Yang Zhongjian, who named the genus, gave it its own family Germanodactylidae. Bennett included the genus in the family Pterodactylidae, and Alexander W.A. Kellner found it to be related to Pterodactylus in his 2003 phylogenetic analysis. David M. Unwin, on the other hand, preferred to consider it a basal dsungaripteroid, a group that evolved into dedicated shellfish-eaters.