Background: Transverse deficiencies of the maxillary basal bone have been treated in adult patients using miniscrew-assisted rapid palatal expansion (MARPE) therapy. However, the midpalatal suture's degree of ossification may affect the upper airway dimensions. This study compared the volumetric changes of the total upper, retropalatal, retroglossal airways, and the minimal transverse airway constriction after MARPE therapy in patients with midpalatal suture in the last stages of ossification. Methods:This controlled clinical trial included a total of 20 adult patients (mean age 24.5 ± 6.2 years) with maxillary atresia treated with MARPE. Preoperative (T0) cone-beam computed tomography scans were used to determine the degree of midpalatal suture ossification. Two groups were formed considering the last two stages of sutural ossification “D” or “E” (n = 10 per group). After 120 days of the therapy (T1), cone-beam computed tomography assessments were performed to compare the pre and post-treatment outcomes. The total upper, retropalatal, and retroglossal airways and the minimal transverse airway constriction were evaluated. The three-dimensional reconstruction was performed with OsiriX MD software. The comparisons were carried out using mixed models for repeated measures at fixed time points (α = 0.05). Results: Groups D and E showed no significant difference for any of the analyzed parameters (P > 0.05). Both groups showed a statistically significant increase for all airway segments after the treatment with MARPE (P < 0.05). The total upper airway increased (11.6% and 16.1%) for groups D and E, respectively (P = 0.3356). Conclusions: MARPE therapy resulted in dimensional gains of the upper airway for adult patients, irrespective of the intermaxillary sutural degree of ossification.