Anatomical and biological specializations have been studied extensively in fossorial rodents, especially in subterranean species, such as mole‐rats or pocket‐gophers. Sciurids (i.e., squirrels) are mostly known for their diverse locomotory behaviors, and encompass many arboreal species. They also include less specialized fossorial species, such as ground squirrels that are mainly scratch diggers. The skull of ground squirrels remains poorly investigated in a fossorial context, while it may reflect incipient morphological specializations associated with fossorial life, especially due to the putative use of incisors for digging in some taxa. Here, we present the results of a comparative analysis of the skull of five fossorial sciurid species, and compare those to four arboreal sciurids, one arboreal/fossorial sciurid and one specialized fossorial aplodontiid. The quantification of both cranial and mandibular shapes, using three dimensional geometric morphometrics, reveals that fossorial species clearly depart from arboreal species. Fossorial species from the Marmotini tribe, and also Xerini to a lesser extent, show widened zygomatic arches and occipital plate on the cranium, and a wide mandible with reduced condyles. These shared characteristics, which are present in the aplodontiid species, likely represent fossorial specializations rather than relaxed selection on traits related to the ancestral arboreal condition of sciurids. Such cranial and mandibular configurations combined with proodont incisors might also be related to the frequent use of incisors for digging (added to forelimbs), especially in Marmotini evolving in soft to hard soil conditions. This study provides some clues to understand the evolutionary mechanisms shaping the skull of fossorial rodents, in relation to the time spent underground and to the nature of the soil.