Treatment effects occurring during Class II malocclusion treatment with the clear aligner mandibular advancement protocol were evaluated in two growing patients: one male (12 years, 3 months) and one female (11 years, 9 months). Both patients presented with full cusp Class II molar and canine relationships. Intraoral scans and cone-beam computed tomography were acquired before treatment and after mandibular advancement. Three-dimensional skeletal and dental long-axis changes were quantified, in which the dental long axis was determined by registering the dental crowns obtained from intraoral scans to the root canals in cone-beam computed tomography scans obtained at the same time points. Class II correction was achieved by a combination of mandibular skeletal and dental changes. A similar direction of skeletal and dental changes was observed in both patients, with downward and forward displacement of the mandible resulting from the growth of the mandibular condyle and ramus. Dental changes in both patients included mesialization of the mandibular posterior teeth with flaring of mandibular anterior teeth. In these two patients, clear aligner mandibular advancement was an effective treatment modality for Class II malocclusion correction with skeletal and dental effects and facial profile improvement.