Background: Proposed skeletal changes achieved by functional appliances (FA) with reference to stable structures (structural method) have received relatively little attention compared to conventional cephalometric measurements (conventional method). Using the two methods, the aims of this study were to (1) determine the skeletal changes as a result of FA treatment; and (2) identify the skeletal changes associated with upper-airway volume and minimum cross-sectional area (MCA). Methods: Pre-and post-treatment CBCT scans were selected from 73 FA treated children (37 girls and 36 boys; mean age 12.0 years) and 73 children as a control group (matched for chronological age, skeletal age, gender, and mandibular inclination) who received orthodontic treatment using only fixed appliances (no FA). Skeletal, upper-airway volume, and MCA changes were analysed by applying both structural and conventional methods. Results: The FA group had significant skeletal effects compared with the control group (both methods; p = 0.04 – p < 0.001). The horizontal displacement of pogonion (both methods) and the hyoid bone, together with a forward mandibular rotation (structural method), had positive effects on upper-airway volume and MCA (p <0.05). Conclusions: The horizontal changes in pogonion (both methods) and the hyoid bone, as well as a forward mandibular rotation (structural method), have a strong association with changes in the upper airway. The conventional method underestimates FA treatment effects. These results may influence the management of growing class II patients with compromised upper airways.