The present case report describes the clear aligner treatment of a 26-year-old woman with maxillary molar distalisation for correction of a unilateral full cusp Class II malocclusion and severe dental midline discrepancy. The patient had previously undergone orthodontic treatment, with her maxillary right first premolar, maxillary left canine and mandibular right first premolar having already been extracted. She presented with a full cusp Class II molar relationship on the right side and a cusp-to-cusp Class II molar relationship on the left. The maxillary dental midline deviated 2 mm to the left whereas the mandibular dental midline deviated 5 mm to the right, resulting in a total midline discrepancy of 7 mm. Invisalign clear aligners (Align Technology, San Jose, CA, USA) were used for orthodontic treatment and the therapy involved molar distalisation and interproximal reduction in the maxilla, extraction of the mandibular left first premolar and molar mesialisation in the mandible. After 30 months of active treatment, a Class I molar relationship was achieved with almost coincident maxillary and mandibular dental midlines. The present case report demonstrates that clear aligners can be an effective tool even in complicated cases.