A new unusual tapejarid pterosaur from the Early Cretaceous Romualdo Formation (Araripe Basin, Brazil) is described, based on a skull, lower jaw and some postcranial elements. Caupedactylus ybaka gen. et sp. shows the typical high nasoantorbital fenestra of the Thalassodrominae but lacks a palatal ridge, and shares with the Tapejarinae several features, including a downturned rostral end, allowing its allocation to that clade. Furthermore, the new species differs in having an anteriorly and posteriorly expanded premaxillary sagittal crest, the lacrimal process of the jugal strongly inclined, and a slit-like postpalatine fenestra, among other characters. The region of the left jugal-quadratojugal-quadrate shows a pathology that is likely the result of an infection. The lateral surface of the premaxillary crest presents grooves that were interpreted in other pterosaurs as impressions of blood vessels, corroborating growing evidence that cranial crests could have been involved in thermoregulation. Also, the new species has a well-preserved palate with a large palatine forming the anterior region of the choanae and the postpalatine fenestra and a secondary subtemporal fenestra. Since the latter has been regarded as unique to non-pterodactyloids, its occurrence in Caupedactylus demonstrates that the evolution of palatal region in pterosaurs is more complex than previously thought.