The present case report describes the treatment of a 25-year-old woman using clear aligners to correct midline deviation and molar tipping caused by tooth loss. The patient’s maxillary left second premolar and mandibular right first molar had been missing for approximately 10 years without having been restored, and the teeth next to the edentulous space were tipped and rotated. She presented with a Class II malocclusion on both sides, with a Class II canine relationship on the right and a Class I canine relationship on the left. The maxillary midline deviated 1.5 mm to the left and the mandibular midline deviated 2.0 mm to the right, giving a total midline discrepancy of 3.5 mm. The treatment involved extraction of the maxillary right second premolar, distalisation of the mandibular left molars, interproximal reduction of the mandibular left anterior teeth and mesialisation of the mandibular right second molar. During treatment, a power arm bent with 19 to 25 mm stainless steel wire was used with maxillomandibular elastics to upright the second molar. After 35 months of active treatment, a full-cusp Class II molar relationship and Class I canine relationship were obtained, and the maxillary and mandibular midlines were consistent with the facial midline. This case report demonstrates that clear aligners can be used to correct more complex cases of malocclusion.