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Dynamic navigation systems were introduced to facilitate dental implantology by improving the accuracy of dental implant positioning. Dynamic navigation integrates surgical instrumentation and radiologic images by using an optical positioning device controlled by a dedicated computerized interface. These features could help in reducing the risk of unintentional iatrogenic damage to nearby anatomic structures and perform minimally invasive or flapless surgery, leading to reduced patient postoperative discomfort and improved healing. The present case report showed the use of the Navident dynamic navigation system (ClaroNav, Toronto, Ontario, Canada) by an undergraduate student for bone cavity preparation and root-end resection in the surgical endodontic treatment of a lesion in an upper lateral incisor. The system allowed precise localization of the root and precise apicoectomy with a minimal invasive cavity. The dynamic navigation system allowed the student to precisely direct the bur in 3 dimensions. The osteotomy and root-end resection were easily and quickly performed by the undergraduate student with a minimally invasive approach without iatrogenic errors. The navigation system allowed the operator to precisely perform a minimally invasive osteoctomy and root-end resection during endodontic surgery. The development of dedicated surgical navigation systems for endodontic surgery could facilitate the operator’s maneuvers and reduce the risk of iatrogenic errors.