Purpose: The purpose of this study was 1) to compare condyle - fossa relationships in the temporomandibular joint (TMJ), and 2) to score condylar resorption by using a TMJ indexing system in patients with JIA and without JIA. Methods: The present retrospective cross-sectional study included cone-beam computed tomography (CBCT) images obtained from the sagittal, coronal, and axial slices. In the multidisciplinary Pediatric Rheumatology Outpatient Clinic at The University of Alabama at Birmingham (UAB) children with JIA are also examined by a group of orthodontists working in the same institute from October 2018 to July 2019. The predictor variable consists of patients with JIA and without JIA. The primary outcome variables are the depth of the mandibular fossa, joint spaces, axial angles, medio-lateral width, and condyle resorption. Other study variables were age and sex. In this study, the measurements obtained from 2 different groups (with JIA and without JIA) are compared using a t-test, where Tukey is utilized to adjust for multiple comparisons. The left and right joints are analyzed separately as the paired t test conducted showed a significant difference between the 2 joints (P < .05). Results: The study was comprised of 34 patients diagnosed with JIA and 34 healthy subjects. The depth of the mandibular fossa, the anterior joint spaces, the axial angles, and the resorption index showed statistically significant differences between the JIA and healthy groups in both left and right sides (P < .05). However, there was no statistically significant difference in the posterior joint spaces and mediolateral width between JIA and healthy groups in both sides (P > .05). Conclusions: The results of our study presented the destructive potential of juvenile idiopathic arthritis by using CBCT. CBCT scanning is a helpful tool in the evaluation of the radiographic result of TMJ.