(1) The purpose of this study is to relate the bidimensional and tridimensional measures of the palate to the vertical facial pattern defined by the angle “SN-MP” between the mandibular plane and the anterior cranial base (Sella–Nasion/mandibular plane angle) in skeletal Class II untreated patients. Furthermore, the same palatal measures were used to compare Class II with Class I subjects. (2) A sample of 197 Class II Caucasian subjects (112 females and 85 males) with untreated skeletal Class II was collected retrospectively (from a private dental clinic specialized in orthodontics) and divided into two main groups according to the ANB angle: 74 Class I patients (0° ≤ ANB ≤ 4°) and 123 Class II patients (ANB > 4°). Class II subjects were furthermore divided into three groups depending on the angle SN-MP. Lateral cephalograms and digital 3D maxillary dental scans were available. Bidimensional and tridimensional measures were taken on each maxillary dental scan. The differences among the groups were analyzed for significance using a variance analysis. (3) A decrease in the posterior palatal height and an increase in the palatal surface area in Class I subjects were reported. The results showed a change in upper arch form, with a greater intermolar width in patients with a low SN-MP angle and a smaller one in high-angle patients. The more a Class II subject tended towards high-angle divergence, the narrower the palate was. (4) A greater posterior palatal height was found in Class II malocclusion, while greater surface area was noted in Class I malocclusion. In addition to this result, another statistical significance was detected in Class II malocclusion: the intermolar distance was greater in hypodivergent than in hyperdivergent patients. Similar volume values were noted across different malocclusions and vertical divergence groups. Palatal width seemed to be related to vertical facial pattern, while palatal height and area seemed to be related to sagittal malocclusions. These findings underscore the importance of considering palatal morphology variations in designing individualized orthodontic treatments, thereby improving patient-specific outcomes and broadening our understanding of skeletal Class II malocclusion.