The aim of this study was to investigate the correlation between craniofacial morphology, temporomandibular joint (TMJ) characteristics, and condylar functional movement in patients with facial asymmetry using an up-to-date automated real-time jaw-tracking system. A total of 30 patients with mandibular asymmetry and prognathism were included. Three-dimensional (3D) craniofacial and TMJ morphometric variables were analyzed in images captured using cone-beam computed tomography. Three-dimensional condylar movements were recorded during the opening, protrusion, and laterotrusion of the jaw and divided into those for deviated and non-deviated sides. Overall functional and morphometric variables were compared between the sides by a paired t-test. Pearson’s correlation analysis and factor analysis were also performed. As a result, significant differences were found between the sides in morphometric and functional variables. The condylar path length was significantly longer and steeper on the deviated side during protrusion and lateral excursion. TMJ morphometric asymmetry, more so than the craniofacial morphologic asymmetry, seemed to be reflected in the functional asymmetry, representing different correlations between the sides, as supported by factor analysis. This study provides evidence explaining why the asymmetric condylar path remained unchanged even after orthognathic surgery for the correction of craniofacial asymmetry.