Ludodactylus is based on holotype SMNK PAL 3828, a skull missing part of the head crest, that was removed from the plate before the fossil was illegally sold. Unlike other ornithocheirids, it had no premaxillary crest on the snout, but did have a crest at the back of the skull. Frey et al. interpreted the deep mandible as a crest on the lower jaws. Trapped between the rami of the mandible is a yucca leaf; Frey suggested that the animal got it caught in its beak and unsuccessfully tried to dislodge it (the edge of the leaf is frayed), and then possibly died from starvation or a complication of starving. The skull would have been more than 66 cm (26 in) long.
Frey et al. in 2003 classified Ludodactylus in the family Ornithocheiridae. In 2007 Frey, had reconsidered the validity of Ludodactylus, suggesting that it may represent the same animal as, and be a junior synonym of, Brasileodactylus. However, Andres & Myers (2013), in a large cladistic analysis of pterosaurs, found Ludodactylus to be slightly more closely related to ornithocheirids and anganguerids than to Brasileodactylus. In the analysis of Andres and Myers, Ludodactylus is classified just outside Ornithocheiridae and Anhangueridae as a derived member of the more inclusive group Pteranodontoidea.