New 3D digital technologies can be applied to implant-supported ear prostheses to restore anatomical structures damaged by cancer, dysplasia, or trauma. However, several factors influence the accuracy of implant positioning using a cranial template. This pilot study describes an innovative navigated flapless surgery for craniofacial implants, prosthetically guided by 3D planning of the ear prosthesis. Laser surface scanning of the face allowed for mapping of the healthy ear onto the defect site, and projection of the volume and position of the final prosthesis. The projected ear volume was superimposed on the skull bone image obtained by cone-beam computed tomography (CBCT), performed with the navigation system marker plate positioned in the patient's mouth. The craniofacial implants were fitted optimally to the ear prosthesis. After system calibration, real-time navigated implant placement based on the virtual planning was performed with minimally invasive flapless surgery under local anesthesia. After 3 months of healing, digital impressions of the implants were made, and the digital manufacturing workflow was completed to manufacture the ear prosthesis anchored to the craniofacial implants. The proposed digital method facilitated implant positioning during flapless surgery, improving the ear prosthesis manufacturing process and reducing operation time, patient morbidity, and related costs. This protocol avoids the need for a reference tool fixed in the cranial bone, as is usually required for maxillofacial surgery, and confirmed that surgical navigation is useful for guiding the insertion of craniofacial implants during flapless surgery.