Background/Objectives: Natural head position (NHP) is an important reference for orthodontic and orthognathic assessment. Although postoperative changes in head posture have been reported previously, simultaneous three-dimensional changes across yaw, pitch, and roll in different skeletal classes remain incompletely characterized. This exploratory study quantified six-month changes in three-dimensional head orientation and compared their direction and magnitude between skeletal Class II and Class III patients. Methods: Fifty-four adults (17 Class II, 37 Class III) undergoing Le Fort I osteotomy and bilateral sagittal split osteotomy were evaluated preoperatively (T0) and 6 months postoperatively (T1). Standardized 3D facial surface acquisitions were obtained using a calibrated structured-light scanner and a fixed external Cartesian laser reference. T0 and T1 datasets were registered using stable upper-facial landmarks (nasion and bilateral exocanthia), and changes in yaw, pitch, and roll were calculated within the common external reference system. Results: Statistically significant T0–T1 changes were observed across all three axes in both skeletal groups (p < 0.01). Class II patients showed mean changes of +2.28° in yaw, −1.30° in pitch, and +2.89° in roll, whereas Class III patients showed +4.61°, +1.96°, and +4.04°, respectively. Between-group differences were significant for yaw, pitch, and roll, with an opposite mean pitch direction and larger mean yaw and roll changes in Class III. Conclusions: At six months, this retrospective cohort demonstrated direction-specific changes in three-dimensional head orientation. Because repeated acquisitions, study-specific observer-reliability and measurement-error analyses, an untreated comparator, an independent validation cohort, and functional or patient-reported outcomes were not available, the findings should be interpreted as exploratory measurements rather than evidence of physiological normalization, neuromuscular adaptation, or clinical benefit. Formal prospective validation is required before the workflow can support predictive or patient management recommendations.