This case report illustrates the successful nonsurgical and nonextraction treatment of a 12-year-old boy with skeletal Class II deep bite malocclusion undergoing two-phase clear aligner treatment. During A6 mandibular advancement phase, Class II buccal segment relationship was corrected by differential forward growth of the mandible, unplanned distalization of maxillary posterior teeth, and unplanned mesialization of mandibular posterior teeth. The maxillary sagittal curve of occlusion was deepened, the mandibular curve of Spee was not fully levelled, and the maxillary arch experienced downward-backward rotation resulting in premature contact on anterior and posterior open bite. Buccal crown tipping of maxillary posterior teeth was observed after arch expansion. The forward growth of the mandible improved the skeletal relationship, and the advancement of the chin position and sagittal movements of the incisors altered the nose-lip-chin relationship, resulting in an improved profile of the patient. During refinement phase, the posterior open bite was corrected. The mandibular plane angle did not increase throughout the treatment. The patient was satisfied with the aesthetic and functional outcome.