This study evaluated the application of digital templates to guide custom-made total temporomandibular joint (TMJ) replacement. Patients treated with a custom-made total TMJ prosthesis for TMJ osteoarthrosis, ankylosis, or tumours were included prospectively. Before surgery, two types of digital template (articular eminence and condyle neck templates) were designed to guide the bone osteotomy and prosthesis positioning. The reconstructive outcomes were assessed through clinical examinations and accuracy analysis by superimposing the postoperative three-dimensional craniomaxillofacial model onto the preoperative virtual plan. Thirty-seven patients (45 joints) underwent successful TMJ reconstruction with the custom-made TMJ prosthesis guided by the digital templates, without intermaxillary fixation. For all patients, the occlusal relationship was stable in reference to the preoperative state. There were significant improvements in pain and maximum inter-incisal opening. Through merging of the pre- and postoperative craniomaxillofacial models, the maximum implanted error was 1.17 ± 0.23 mm in linear measurement and 1.19 ± 0.14 mm in surface deviation. There was more deviation in the anteromedial part of the fossa and inferior part of the mandibular handle. The digital templates were able to assist in the accurate placement of the TMJ prosthesis without the need for intermaxillary fixation.