The skeletal and dental effects of rapid maxillary expansion (RME) have been extensively studied, but high-quality research is still needed to determine the three-dimensional (3D) effects of RME. The aim of this study was to compare skeletal and dentoalveolar parameters through cone-beam computed tomography (CBCT) pre- (T1) and post-treatment (T2) with respect to RME. Twenty growing patients (mean age 10.7 years) were treated with a Hyrax-type expander. A 3D CBCT was performed at T1 and T2, measuring nasal width, maxillary width, palatal height, maxillary arch perimeter, angulation of the upper first molar, and intermolar width. The mean palatal suture opening was 2.85 ± 0.62 mm (p < 0.0001). Nasal width increased 1.28 ± 0.64 mm and maxillary width 2.79 ± 1.48 mm (p < 0.0001). In contrast, palatal height was reduced 0.65 ± 0.64 mm (p < 0.0001). Regarding arch perimeter, the radicular perimeter increased 2.89 ± 1.80 mm, while the coronal perimeter increased 3.42 ± 2.09 mm (p < 0.0001). Molar angulation increased 5.62 ± 3.20° for the right molar and 4.74 ± 2.22° for the left molar (p < 0.0001). Intermolar width increased 5.21 ± 1.55 mm (p < 0.0001). Treatment with Hyrax produced a significant opening in the mean palatal suture. Also, a significant increase in nasal width, maxillary width, arch perimeter, molar angulation, and intermolar width, and a decrease in palatal height, were observed.