The aim of this study was to assess the maxillary arch asymmetry in paediatric subjects with functional posterior crossbite. Linear widths and depths of maxillary hemi-arches were measured in crossbite patients (29 girls, 14 boys; mean age: 9.49 ± 1.22 years) and in a control group (26 girls, 18 boys; mean age: 9.35 ± 0.70 years) without crossbite. Differences in the linear widths and depths between the two maxillary sides were analysed and compared between groups. Additionally, a 3D superimposition of the mirrored maxillary models was performed for each subject to evaluate dental–alveolar and palatal vault-matching percentages and compare between groups. The Mann–Whitney U test was used for the statistical analysis. The differences in the maxillary hemi-arch linear distances between the two sides of the maxilla were significantly greater in the study group than in the control group (p = 0.000). Matching percentages of the upper arch were lower in the crossbite group (p = 0.000), particularly in the dental–alveolar region of the molars. These findings indicate that maxillary asymmetry in both the transverse and sagittal dimensions is more pronounced in crossbite patients, and the deviations between the two maxillary halves are more evident at the dental–alveolar level and in the molar region.