Comparison of birds and pterosaurs, the two archosaurian flyers, sheds light on adaptation to an aerial lifestyle. The neurological basis of control holds particular interest in that flight demands on sensory integration, equilibrium, and muscular coordination are acute. Here we compare the brain and vestibular apparatus in two pterosaurs based on high-resolution computed tomographic (CT) scans from which we constructed digital endocasts. Although general neural organization resembles birds, pterosaurs had smaller brains relative to body mass than do birds. This difference probably has more to do with phylogeny than flight, in that birds evolved from nonavian theropods that had already established trends for greater encephalization. Orientation of the osseous labyrinth relative to the long axis of the skull was different in these two pterosaur species, suggesting very different head postures and reflecting differing behaviours. Their enlarged semicircular canals reflect a highly refined organ of equilibrium, which is concordant with pterosaurs being visually based, aerial predators. Their enormous cerebellar floccular lobes may suggest neural integration of extensive sensory information from the wing, further enhancing eye- and neck-based reflex mechanisms for stabilizing gaze.