Introduction: The temporomandibular joint (TMJ) is affected in 30–45% of juvenile idiopathic arthritis (JIA) patients, with all JIA subtypes at risk for TMJ involvement. JIA patients with TMJ involvement may present with altered craniofacial morphology, including micrognathia, mandibular retrognathia, a hyperdivergent mandibular plane angle, and skeletal anterior open bite. These features are also commonly present and associated with non-JIA pediatric patients with obstructive sleep apnea (OSA). Materials and Methods: The study was comprised of a group of 32 JIA patients and a group of 32 healthy control subjects. CBCT images were taken for all patients and were imported into Dolphin Imaging software. The Dolphin Imaging was used to measure the upper airway volumes and the most constricted cross-sectional areas of each patient. Cephalometric images were rendered from the CBCT data for each patient, and the following cephalometric values were identified: SNA angle, SNB angle, ANB angle, anterior facial height (AFH), posterior facial height (PFH), mandibular plane angle (SN-MP), FMA (FH-MP), overjet (OJ), and overbite (OB). Airway volumes, the most constricted cross-sectional area values, and cephalometric values were compared between the JIA and control groups. Results: For airway values, statistically significant differences were seen in the nasopharynx airway volume (p = 0.004), total upper airway volume (p = 0.013), and the most constricted cross-sectional area (p = 0.026). The oropharynx airway volume was not statistically significant (p = 0.051). For cephalometric values, only the posterior facial height showed a statistically significant difference (p = 0.024). Conclusions: There was a significant difference in airway dimensions in the JIA patients as compared to the control patients. In addition, the posterior facial dimensions seem to be affected in JIA patients. The ODDs ratio analysis further corroborated the findings that were significant.