Cleft lip and palate is the most common congenital craniofacial anomaly. Up to 60% of these patients will benefit from cleft orthognathic surgery, which consists primarily of maxillary advancement and mandibular setback to address midface retrusion and relative mandibular protrusion, respectively. It is believed that maxillary advancement can enlarge the airway whilst mandibular setback can reduce the airway, but this has not previously been quantified for cleft patients undergoing orthognathic surgery. This unique longitudinal prospective study of 18 patients was conducted between April 2013 and July 2016. No significant changes occurred by six months postoperatively in body mass index, apnoea-hypopnoea index or lowest oxygen saturation (LSAT). There was a mean increase of 0.73 cm3 in velopharyngeal volume, a mean decrease of 0.79 cm3 in oropharyngeal volume, an improvement in snoring index, and no statistically significant change in hypopharyngeal volume. In conclusion, cleft orthognathic surgery that produced anterior advancement of the maxilla, setback of the mandible and clockwise rotation of the maxillo-mandibular complex resulted in increased velopharyngeal, decreased oropharyngeal and unchanged hypopharyngeal airways, and improved snoring, but did not significantly alter objective sleep-related breathing function.