The objective of this study is to introduce the application of augmented reality (AR) navigation system developed by the authors in recontouring surgery of craniofacial fibrous dysplasia. Five consecutive patients with craniofacial fibrous dysplasia were enrolled. Through three-dimensional (3D) simulation, a virtual plan was designed to reconstruct the normal anatomical contour of the deformed region. Surgical recontouring was achieved with the assistance of the AR navigation system. The accuracy of the surgical procedure was assessed by superimposing the post-operative 3D craniomaxillofacial model onto the virtual plan. The pre-operative preparation time and operation time were also counted. In all patients, AR navigation was performed successfully, with a mean ± SD of the errors of 1.442 ± 0.234 mm. The operative time of the patients ranged from 60 to 80 min. The pre-operative preparation time was 20 min for each patient. All the patients showed uneventful healing without any complications, in addition to satisfaction with the post-operative aesthetics. Using our AR navigation system in recontouring surgery can provide surgeons with a comprehensive and intuitive view of the recontouring border, as well as the depth, in real time. This method could improve the efficiency and safety of craniofacial fibrous dysplasia recontouring procedures.