Transnasal surgical treatment of congenital choanal atresia is difficult. A limited view to the surgical field often accounts for poor results. An occurrence of a restenosis is frequently observed requiring difficult revision surgery. Severe complications include bleeding, skull base and intracranial injuries as well as orbital injuries. We describe the use of an optical computed tomography data-based navigation system for surgical planning and intraoperative guidance to improve treatment outcome. Computer-assisted planning and computed tomography data-based navigation was used in the case of a 2-year-old infant with a history of Treacher Collins syndrome associated with bilateral choanal atresia. To reduce target registration error, registration markers were fixed to a maxillary dental splint that was inserted intraorally during image data acquisition and patient registration. A combined technique using navigational guidance and nasal and retropalatal endoscopy was used for instrument navigation successfully removing the bony atretic plates. This clinical report demonstrates the feasibility of a combined approach with surgical navigation. A larger clinical series with long-term follow up will be needed to determine the reproducibility and validation of potential benefits.