Congenital aural atresia repair is difficult owing to unpredictable anatomy. Benefits may be gained from computer-aided surgery (CAS), but its exact role has yet to be clearly defined. This is a retrospective study of 18 patients with bony type C (Schuknecht classification) congenital atresia. In the first group (n = 9), repair was performed with CAS while in the second group (n = 9), similar intervention was applied without CAS. Intra- and post-operative clinical and audiological findings were compared. CAS computed tomography (CT) images correlated well with intra-operative findings giving the surgeon more security and reducing operative time by 25 minutes. In our estimation, CAS is valuable for type C congenital aural atresia repair. It serves as an educational tool and as a guide for the experienced surgeon in critical situations where anatomical landmarks are distorted and where access is limited.