This randomized clinical trial aimed to compare the three-dimensional dentoalveolar maxillary changes after anterior open bite treatment with bonded spurs and build-ups versus bonded spurs alone. Patients from 7 to 11 years of age with anterior open bite were randomly allocated into two groups. Bonded spurs and posterior build-ups were used in the experimental group and only bonded spurs were used in the comparison group. The randomization sequence was generated at www.randomization.com. Opaque, sealed and sequentially numbered envelopes were part of the allocation concealment. Digital dental models were acquired before (T1) and after 12 months of treatment (T2) and de-identified for analysis purposes. Three-dimensional changes of maxillary permanent incisors and first molars were evaluated by means of T1 and T2 dental model superimposition. Landmark-based registration on the posterior teeth and registration on the palate using regions of interest were performed. T or Mann–Whitney U tests were used for intergroup comparisons (P < 0.05). Mean difference (MD) and 95% confidence interval (CI) were calculated. Twenty-four children (17 girls and 7 boys) were included in the experimental group (mean age 8.22 ± 1.06 years) and 25 children (14 girls and 11 boys) were included in the comparison group (mean age 8.30 ± 0.99 years). After 12 months of treatment, inferior displacements of maxillary incisors were similar in the experimental (1.55–2.92 mm) and comparison (1.40–2.65 mm) groups. Inferior displacement of the maxillary molars was also similar in both groups (MD: − 0.13 mm; 95% CI − 0.38, 0.12). The experimental and comparison groups showed medial and lateral displacements of the permanent first molars, respectively (MD, − 0.31 mm; 95% CI − 0.51, − 0.11). Lingual inclination of the permanent first molars were observed in the experimental group and buccal inclination in the comparison group (MD, − 2.16°; 95% CI − 3.72, − 0.60). Similar three-dimensional displacements of maxillary central and lateral incisors, and inferior displacements of maxillary permanent first molars were observed in both groups. Bonded spurs associated with posterior build-ups demonstrated some medial displacement and lingual inclination of the maxillary permanent first molars while opposite changes were noticed in the comparison group. Trial registration: Clinicaltrials.gov; NCT03702881, date of registration: October 11, 2018.