A complete skull of Ursus deningeri recovered from the Middle Pleistocene site of the Sima de los Huesos in the Sierra de Atapuerca (Spain) was studied with computed tomography. This technique makes it possible to study new and relevant information in the endocranial structures and avoids any damage to the specimen. The previously undescribed endocranial cavity of U. deningeri is compared with related species such as Ursus spelaeus Rosenmüller 1794 and Ursus arctos Linné 1758. The characters analyzed include the braincase morphology and also quantitative and volumetric measurements, which are only attainable with this technique. In particular, the volume, surface area, and form of the frontal sinuses and brain cavity, the shape of the ethmoid bone, and the basioccipital pneumatization were studied. The resulting analysis supports an ancestor-descendant relationship for the two ursids included in the cave bear phylogenetic lineage (U. deningeri and U. spelaeus). In contrast, U. arctos exhibits a different endocranial morphology, one that seems to be mainly plesiomorphous. Finally, this study has identified several new endocranial characters which are useful in reconstructing ursid phylogeny.