Orthognathic surgery is indicated to modify the position of the maxillomandibular structure; changes in the mandibular position after osteotomy can be related to changes in the position of the mandibular condyle in the articular fossa. The aim of this study was to determine changes produced in the mandibular condyle 6 months after orthognathic surgery. A cross-sectional study was conducted that included subjects who had undergone bimaxillary orthognathic surgery to treat dentofacial deformity of Angle class II (group CII) or Angle class III (group CIII). Standardized images were taken using cone-beam computed tomography 21 days before surgery and 6 months after surgery; measurement scales were used to identify the condylar position and its relations with the anterior, superior, and posterior joint spaces. The results were analyzed using the Shapiro–Wilk and Student’s t-tests, while considering a value of p < 0.05 as indicating a significant difference. Fifty-two joints from 26 patients, with an average age of 27.9 years (±10.81), were analyzed. All subjects in both group CII and group CIII showed a significant change in the anterior, superior, and posterior joint spaces. However, postoperative changes in the position of the condyle in the articular fossa were not significant in the anteroposterior analysis. We conclude that orthognathic surgery causes changes in the sagittal position of the mandibular condyle in subjects with mandibular retrognathism and prognathism.