Craniosynostosis must often be corrected using surgery, by which the affected bone tissue is remodeled. Nowadays, surgical reconstruction relies mostly on the subjective judgement of the surgeon to best restore normal skull shape, since remodeled bone is manually placed and fixed. Slight variations can compromise the cosmetic outcome. The objective of this study was to describe and evaluate a novel workflow for patient-specific correction of craniosynostosis based on intraoperative navigation and 3D printing. The workflow was followed in five patients with craniosynostosis. Virtual surgical planning was performed, and patient-specific cutting guides and templates were designed and manufactured. These guides and templates were used to control osteotomies and bone remodeling. An intraoperative navigation system based on optical tracking made it possible to follow preoperative virtual planning in the operating room through real-time positioning and 3D visualization. Navigation accuracy was estimated using intraoperative surface scanning as the gold-standard. An average error of 0.62 mm and 0.64 mm was obtained in the remodeled frontal region and supraorbital bar, respectively. Intraoperative navigation is an accurate and reproducible technique for correction of craniosynostosis that enables optimal translation of the preoperative plan to the operating room.