Skeletal Class III malocclusion represents a significant challenge in orthodontics due to its impact on facial aesthetics and function, particularly in patients with limited residual growth. Bone-anchored maxillary protraction (BAMP) with miniplates has emerged as an effective alternative to conventional orthopaedic approaches, providing greater skeletal effects with less dentoalveolar compensation. This study reports the clinical management of a patient with limited growth potential and skeletal Class III malocclusion, treated with miniplate-assisted maxillary protraction followed by aligner therapy. A 9-year-8-month-old female patient, presenting with maxillary retrusion and mild mandibular protrusion (SNA = 79.2°, SNB = 80.8°, ANB = −1.6°, AO-BO = −11.1 mm), was treated with four Bollard miniplates and Class III elastics for 9 months. The orthopaedic phase resulted in significant maxillary advancement (SNA increased to 85.1°), improved sagittal relationship (ANB increased to 3.5°), and improved Wits score from −11.1 mm to 1.8 mm, with minimal changes in mandibular position. Structural overlays demonstrated that the maxillary advancement achieved during the orthopaedic phase was accompanied by vertical mandibular development during the orthodontic phase, thereby favourably redirecting the initial hypodivergent pattern and improving facial balance. Subsequent orthodontic refinement was performed with clear aligners, totalling 130 aligners in multiple refinement stages, leading to Class I relationships in the canines and molars, improved intercuspation, and correction of midline deviation. Although aligner therapy required multiple refinements, satisfactory functional and aesthetic results were obtained without the need for orthognathic surgery in this case. Maxillary protraction assisted by miniplates followed by aligner therapy was effective for the treatment of this case of skeletal Class III malocclusion.