This retrospective two-centre study aimed to evaluate the occlusal outcomes in patients undergoing orthognathic surgery with clear aligners. A retrospective chart review and occlusal outcomes for 15 patients (10 females and five males) with different types of dentofacial deformities in the anteroposterior, vertical and transverse dimensions, who underwent orthognathic surgery in conjunction with clear aligners were evaluated. Weighed Peer Assessment Rating (PAR) index scores of the pre-treatment and post-treatment digital models were used to assess initial complexity, final occlusal outcomes and degree of improvement with surgery and clear aligners. The mean post-treatment PAR score was 3.5± 2.54, which was a statistically significant improvement from the pre-treatment PAR score of 27.63 ± 12.09, an 87% improvement was achieved. All subcategories of the PAR index showed statistically significant improvement except for midline assessment component. Occlusal outcomes with aligners showed great improvement as indicated with the PAR index scores. Orthognathic surgical cases can be treated efficiently with aligners and future studies should compare occlusal outcomes between orthognathic surgical patients treated with clear aligners and those treated with fixed appliances.