When conventional endodontic treatment resources are depleted, endodontic surgery becomes an alternative treatment for apical periodontitis to remove unreachable infected areas and seal the root canal. Digital workflows have been used more frequently in many dental applications in recent years. In endodontics, virtual 3-dimensional (3D) planning and endodontic guidance are new aspects important for the treatment of complex cases. This report aimed to present 3D Apicoectomy Guidance, a novel method of performing guided ultraconservative endodontic surgery with conventional implant-guided drills, and to describe its application in a case with a complex anatomic scenario and intimate contact with the maxillary sinus. Implantology computer software, as well as cone-beam computed tomography images and a digital scanning 3D impression, enabled virtual planning of the surgical procedure. Subsequently, a 3D template was produced to guide the instruments used in the osteotomy and root resection. The patient was completely asymptomatic at the 1-week follow-up visit. Cone-beam computed tomography scans were performed at 1 and 6 months after surgery and showed that resection of the apex of the root was performed accurately and that a thin dentin slice remained distally, preventing the rupture of the sinus membrane. The patient remained asymptomatic, and the tissue healed normally. The method used was shown to be very straightforward and reliable. This method allowed the patient to be treated expeditiously with very precise tissue removal.