Background: The aim was to assess three-dimensionally mandibular and maxillary changes in growing Class II patients treated with removable functional appliances followed by fixed appliances. Methods: Twenty-four Class II patients (age range: 9 to 14, mean: 12.1 ± 1.1 years) treated with removable functional appliances followed by fixed appliances (functional appliance group—FAG) were retrospectively selected and compared to an age-matched control group (CG) treated with fixed appliances only. To be included in the study, pre- and post-treatment CBCT scans had to be available. The CBCTs were used to analyze, in 3D, the changes following treatment and growth. Results: Before treatment, overjet (FAG: 9 mm ± 2.8 (mean ± standard deviation); CG: 4 mm ± 1.7), ANB (FAG: 5.7° ± 2.0; CG: 3.2° ± 1.4), and effective mandibular length (FAG: 113.0 mm ± 4.1; CG: 116.6 mm ± 5.9) were statistically significantly different between the two groups. After treatment, overjet (FAG: −6.8 mm ± 2.8; CG: −1.8 mm ± 1.8) and effective mandibular length (FAG: 6.3 mm ± 2.6; CG: 3.9 mm ± 2.6) statistically significantly changed. There was a significant difference in the treatment effect between the FAG and the CG in overjet, ANB, and effective mandibular length. Conclusions: The results indicate that functional appliances are effective in correcting Class II malocclusions. The growth modification in the FAG resulted in an increase in mandibular length. Yet, the final length of the mandible in the FAG was smaller when compared to the CG.