This case report describes a 19-year-old man presented with a 5.7-mm deep overbite, Class II division 2 malocclusion with the right upper maxillary canine completely buccal ectopia, deviated midline in the upper arch, severe crowding and retroclination of the maxillary and mandibular incisors. The patient was treated with clear aligners to correct the Class II relationship and the deep overbite. A series of clear aligners were used to move bilateral maxillary molars distally with unilateral mini-screw anchorage. The final results showed that clear aligners with mini-screws could effectively achieve the required upper distal molar movement thanks to a reasonable design of the stages and anchorage. The treatment was completed in 19 months and the patient was satisfied with the treatment outcome in this context of mild to moderate Class II division 2 malocclusion.