Minimally-invasive surgery (MIS) for stent implantation is a complex procedure requiring specialized instruments. It often leads to prolonged patient recovery, and interrupted operations due to incorrect instrument selection and complex anatomy. This study presents a novel magnetic navigation system that addresses these challenges by using magnetic fields and computed tomography imaging to precisely navigate minimally-invasive surgical guidewires. The system is designed based on consultations with surgeons, and analysis of technical and clinical requirements of stent implantation procedures. Results from a human-in-the-loop case study with eleven operators indicate a 47% reduction in guidewire navigation times, while successfully reaching all predetermined luminal targets. The clinical relevance, usability, and operator satisfaction are also measured using a user experience questionnaire, and interviews and showed positive results. Compared to conventional, manual guidewire navigation, the magnetic navigation system has the potential to significantly impact the efficiency of the clinical workflow and improve complex endovascular aortic repair procedures.