Introduction: Although functional appliances (FAs) are primarily used to treat Class II malocclusions, their effects on the upper airway have generally been reported in studies involving 2-dimensional analysis of cephalometric radiographs. This study aimed to use 3-dimensional cone-beam computed tomography to (1) determine the effects on upper airway volume and minimum cross-sectional area (MCA) when an FA is used for orthodontic treatment and (2) identify pretreatment markers for airway changes. Methods: Pre- and posttreatment cone-beam computed tomography scans were selected from 73 children whose orthodontic treatment involved using a fixed FA (37 girls and 36 boys; mean age 12.0 years); a control group was constituted and included the scans of 73 children who were matched for chronological age, skeletal age, sex, and mandibular inclination and who received orthodontic treatment for minor malocclusions without an FA. Changes in upper airway volume and MCA were evaluated by a standardized, previously validated method analyzed with mixed-effects linear regression. Results: Upper airway volume and MCA increased over time for both the FA and the matched control groups (P <0.05). The FA caused an additional significant increase in upper airway volume and MCA (P <0.0001) when compared with the control group. An increased ANB angle, a reduced mandibular inclination, and a reduced skeletal age pretreatment had a positive effect on upper airway volume and MCA (P <0.05). Conclusions: A fixed FA was associated with a significant increase in upper airway volume and MCA in children when compared with controls. Pretreatment ANB angle, skeletal age, and mandibular inclination may be predictors for positive changes in the upper airway. The results may prove valuable in treating children with Class II malocclusions with compromised upper airways.