Flying squirrels (Sciurinae, Pteromyini) are the most successful group of gliding mammals. However, their fossil record mostly consists of isolated dental remains which provide very limited insights into their paleobiology and evolution. Only recently, the first skeleton of a fossil flying squirrel, belonging to the species Miopetaurista neogrivensis, has been described. It presents all the diagnostic gliding-related postcranial features of its extant relatives and shows that this group has undergone very little morphological change for almost 12 million years. However, the associated cranium is badly crushed, so particular details of the cranial morphology cannot be described. Here we describe a well-preserved cranium of the closely-related Miopetaurista crusafonti from 12.5–12.0 Ma from Bavaria (Germany). Its cranial morphology is found to be almost identical to extant large flying squirrels, even in details such as the position of the foramina. The virtual endocast also shows close affinities to living large flying squirrels in morphology and in the relative volume of different brain regions, showing diagnostic features such as the size reduction of petrosal lobules and olfactory bulbs. However, the encephalization quotient (EQ) and neocortical ratio are lower than observed in extant flying squirrels. EQ is known to increase through time in squirrels, but might also be related to locomotion, as arboreal and gliding squirrels display higher EQs than terrestrial ones. Because Miopetaurista was certainly a glider, its comparatively lower EQ and neocortical size support the existence of an independent trend of increasing EQ and neocortical complexity in this flying squirrel subclade.