Objective: This study aims to (1) assess the facial morphology in juvenile idiopathic arthritis (JIA) subjects with moderate to severe temporomandibular joint (TMJ) involvement using 3D surface scans and (2) compare the facial morphology in these subjects to that in JIA subjects without TMJ involvement. Methods: Sixty JIA subjects were included and grouped as follows: group 1 (no involvement group), JIA without TMJ involvement; Group 2 (unilateral group), JIA with moderate to severe unilateral TMJ involvement; and group 3 (bilateral group), JIA with bilateral TMJ involvement. Standard orientation of all surfaces was accomplished. The means and variabilities of facial morphology in groups 2 and 3 were assessed and compared with those of group 1 in three dimensions, respectively. Results: Group 2 (unilateral group) exhibited a more retruded and wider chin, shorter mandibular height, and more prominent cheek (2, 2, 5, and 2 mm, on average, respectively) on the affected side and a more retruded and narrower chin and more prominent malar region (4, 3, and 2 mm, on average, respectively) on the unaffected side compared with group 1 (no involvement group) (p < 0.05). Group 3 (bilateral group) exhibited a more retruded chin, shorter mandibular height, more prominent upper cheeks, and narrower perioral region (5, 5, 3, and 2 mm, respectively) compared with group 1 (no involvement group) (p < 0.05). Conclusions: In JIA subjects with moderate to severe unilateral or bilateral TMJ involvement, the affected side(s) revealed similar facial dysmorphology with reduced mandibular height, chin retrusion, and prominent upper cheek. Clinical relevance: Three-dimensional surface scans can be a non-ionizing indicator of signs of TMJ involvement in JIA subjects.