Applications of cone-beam computed tomography (CBCT) in orthodontics have been increasingly discussed and evaluated in science and practice over the last two decades. The present work provides a comprehensive summary of current consolidated practice guidelines, cutting-edge innovative applications, and future outlooks about potential use of CBCT in orthodontics with a special focus on upper airway analysis in patients with sleep-disordered breathing (SDB). The present scoping review reveals that clinical applications of CBCT in orthodontics are broadly supported by evidence for the diagnosis of dental anomalies, temporomandibular joint disorders, and craniofacial malformations. On the other hand, CBCT imaging for upper airway analysis—including soft tissue diagnosis and airway morphology—needs further validation in order to provide better understanding regarding which diagnostic questions it can be expected to answer. Internationally recognised guidelines for CBCT use in orthodontics are existent, and similar ones should be developed to provide clear indications about the appropriate use of CBCT for upper airway assessment, including a list of specific clinical questions justifying its prescription.