Objectives: The objective of this study was to examine changes in facial soft tissue asymmetry over time in patients after Class II orthognathic surgery using three-dimensional (3D) stereophotogrammetry. Methods: The study consists of 54 patients with a skeletal Class II malocclusion (32 female, 22 male; mean age, 33.2 years). Three-dimensional photographic data were collected using the 3dMD Trio stereophotogrammetry system. The evaluation of 21 anthropometric landmark positions was conducted before surgery (T0), 6 months (T1), and 12 months (T2) after surgery. Facial asymmetry was classified as mild (0–2 mm), moderate (3–5 mm), or severe (>5 mm). Results: There was a small difference in the mean distance when analyzing the asymmetry of the whole face. The 3D measurements showed statistically significant differences (p < 0.05) between T0 versus T1 and T2 time-point values. Prior to surgery, males exhibited a higher degree of soft tissue asymmetry compared to females. The chin volume asymmetry score was higher in the females of the cohort and patients undergoing bimaxillary surgery (median 1.11) than in the males of the cohort and patients undergoing single-jaw surgery (median 1.08); however, these differences were not statistically different. Conclusions: The findings indicate that soft tissue asymmetry may become altered within a 6-month period following surgery.