Objective: To compare short- and long-term dentoalveolar, skeletal, and rotational changes evaluated by Björk’s structural method of superimposition between children with Class II malocclusion treated by functional appliances and untreated matched controls. Methods: Seventy-nine prepubertal or pubertal children (mean age, 11.57 ± 1.40 years) with Class II malocclusion were included. Thirty-four children were treated using an activator with a high-pull headgear (Z-activator), while 28 were treated using an activator without a headgear (E-activator). Seventeen untreated children were included as controls. Lateral cephalograms were obtained before treatment (T1), after functional appliance treatment (T2), and after retention in the postpubertal phase (T3). Changes from T1 to T2 and T1 to T3 were compared between the treated groups and control group using multiple linear regression analysis. Results: Relative to the findings in the control group at T2, the sagittal jaw relationship (subspinalenasion- pogonion, p < 0.001), maxillary prognathism (sella-nasion-subspinale, p < 0.05), and condylar growth (p < 0.001) exhibited significant improvements in the Z- and E-activator groups, which also showed a significantly increased maxillary incisor retraction (p < 0.001) and decreased overjet (p < 0.001). Only the E-activator group exhibited significant backward rotation of the maxilla at T2 (p < 0.01). The improvements in the sagittal jaw relationship (p < 0.01) and dental relationship (p < 0.001) remained significant at T3. Condylar growth and jaw rotations were not significant at T3. Conclusions Functional appliance treatment in children with Class II malocclusion can significantly improve the sagittal jaw relationship and dental relationships in the long term.