Purpose Adequate control of the vertical dimension is of great importance in orthodontic treatment. Although existing evidence is very limited, extraction of four premolars is thought to contribute towards improved control of anterior facial height compared with non-extraction treatment protocols. Thus, the aim of this retrospective cohort study was to compare the effect of fixed-appliance treatment with extraction of four premolars to non-extraction treatment on the skeletal vertical dimension. Methods A consecutive sample of 76 children with skeletal hyperdivergence (49% male; mean age 11.9 years) was divided into two groups for treatment with either non-extraction (n = 31) or extraction of four premolars (n = 45). Baseline characteristics were comparable: overjet 5.1 ± 2.5 mm, overbite 2.4 ± 1.9 mm, ANB angle 4.6 ± 2.3°, and SN-ML angle 40.2 ± 3.5°. Patients were treated with standard edgewise fixed appliances with closing loops/sliding mechanics. Vertical skeletal and dental outcomes were measured on lateral cephalograms before and after treatment. Data were analyzed with linear regression at 5%. Results Compared to non-extraction treatment, treatment with premolar extractions had no significant effect on the SN-ML angle (difference (Δ) = 0.07°; 95% confidence interval −0.90 to 1.01°; P = 0.88). Statistically significant changes between the extraction and non-extraction groups were only found for the parameters SNA (Δ −1.47°; P = 0.003), ANB (Δ −1.17°; P = 0.004), SN-OP (Δ −1.48°; P = 0.04), and L1-ML (Δ −6.39°; P < 0.001). Conclusion Orthodontic treatment of children with skeletal hyperdivergence using systematic extraction of four premolars had minimal effects on the vertical facial dimension compared to non-extraction treatment.