Facial asymmetry is often seen in patients with skeletal mandibular prognathism and is associated with deformities in the maxillofacial and head regions. The maxillofacial deviation is three-dimensional and affects not only the lateral deviation of the mandible and midface, but also the cranium. This study conducted a three-dimensional morphological evaluation of the cranial base morphology of patients with skeletal mandibular prognathism (ANB < 0°, Wits < 0 mm) with the aim of examining the relationship between deformities of the head region and facial asymmetry. Data obtained from computed tomography conducted during the initial examination of patients with and without skeletal mandibular prognathism with facial asymmetry were used. Differences in the position of structures present in the cranial base were measured, and the association between cranial deformities and mandibular deviation was assessed. The middle cranial base area and the lateral deviation of the mandibular fossa were significantly larger in patients with facial asymmetry compared to those without facial asymmetry. In addition, a correlation between the amount of mandibular deviation and the area of the anterior cranial base was identified in patients with significant cranial deformity (p = 0.012). Given the identified association between the structure of the head region and facial asymmetry, further studies are needed to determine the factors implicated in the growth process.