Background: Sphenoid dysplasia is a distinctive but uncommon manifestation of neurofibromatosis type 1. The absence of the sphenoid greater wing allows the temporal lobe to prolapse into the orbit resulting in temporal base encephalocele and pulsating exophthalmos. Surgical procedures are aimed at preserving vision and improving ocular movement and cosmesis. This defect can be closed using bone grafts or titanium mesh. However, the results of this procedure are often unsustainable due to bone graft resorption and graft displacement. Methods: In this report, we describe a novel surgical technique, combining computer-aided design, stereolithography and neuronavigation to repair a temporal base skull defect in a 16-year-old female patient with neurofibromatosis type 1. A three-dimensional model of the skull base defect and a template for graft were first constructed according to the image data, then transferred to a real-size stereolithographic biomodel using a rapid prototyping technique. Results: The final graft of titanium mesh, which was intraoperatively fabricated based on the biomodel, was precisely orientated and securely fixed to the surrounding bone under frameless navigation. Long-term follow-up result proved this repair to be effective and durable. Conclusion: The approach combining computer-aided design, stereolithography and surgical navigation could help managing the complex lesions in the skull base and craniofacial area requiring rigid reconstruction.