The maxillofacial region of patients with facial asymmetry is deformed not only in the mandible but also in the maxilla, suggesting that the head region may also be deformed. Therefore, in this study, skeletally originated mandibular prognathism with facial asymmetry was evaluated in relation to cranial morphology. The cranial morphology of patients who visited the Chiba Dental Center of Tokyo Dental College and were diagnosed with skeletal mandibular prognathism with facial asymmetry (asymmetry group: ANB 0° or less; Menton deviation 4 mm or more; 30 subjects) and without facial asymmetry (symmetry group: ANB less than 0°; Menton deviation less than 3 mm) was measured and evaluated. As a method, the length and area of the cranium were measured using axial cephalometric radiographs. In the asymmetry group, there was a significant difference in the left–right difference in the long diameter of the posterior part of the cranium compared to the symmetry group (p = 0.009). The asymmetry group also had significant differences in the central and occipital areas of the cranium on the left and right sides compared to the symmetry group (p < 0.001). In the asymmetry group, the direction of Menton deviation and the direction of head region deviation coincided in about 70% of the cases. There was also a positive correlation between head deviation and the amount of Menton deviation. The results of this study suggested that patients with facial asymmetry had greater head deformity than patients without facial asymmetry.