Cranioplasty is considered a simple reconstructive procedure, usually performed in a single stage. In some clinical conditions, such as in children with multifocal flap osteolysis, it could represent a surgical challenge. In these patients, the partially resorbed autologous flap should be removed and replaced with a precustomed prosthesis which should perfectly match the expected bone defect. We describe the technique used for a navigated cranioplasty in a 3-year-old child with multifocal autologous flap osteolysis. We decided to perform a cranioplasty using a custom-made hydroxyapatite porous ceramic flap. The prosthesis was produced with an epoxy resin 3D skull model of the patient, which included a removable flap corresponding to the planned cranioplasty. Preoperatively, a CT scan of the 3D skull model was performed without the removable flap. The CT scan images of the 3D skull model were merged with the preoperative 3D CT scan of the patient and navigated during the cranioplasty to define with precision the cranioplasty margins. After removal of the autologous resorbed flap, the hydroxyapatite prosthesis matched perfectly with the skull defect. The anatomical result was excellent. Thus, the implementation of cranioplasty with image merge navigation of a 3D skull model may improve cranioplasty accuracy, allowing precise anatomic reconstruction in complex skull defect cases.