Background/Objectives: The extraction of impacted mandibular third molars (M3Ms) carries significant risks, especially regarding the inferior alveolar nerve (IAN). This study aimed to evaluate the effectiveness of a 3D-planned inward fragmentation technique (3Dp-IFT) to improve surgical outcomes, reduce complications, and preserve bone structure in cases involving complex M3M impactions. Methods: Twenty-three patients aged between 18 and 36 years requiring M3M removal were included. Preoperative planning involved the use of cone–beam computed tomography (CBCT) for precise localization of the furcation area, followed by the creation of a 3D navigation template using PlastyCAD software version 1.7. The surgical procedure was performed under local anesthesia, with meticulous endoscopic assistance to ensure accurate access and minimize trauma. Postoperative outcomes, such as bone loss, pain, swelling, and mouth opening range, were carefully measured. The data were systematically organized and analyzed descriptively using Microsoft Excel. Results: No disturbances to the IAN or lingual nerve were observed. The mean buccal bone loss was 2.2 mm, with a standard deviation of 1.2 mm. Postoperative pain and swelling were generally low, with significant reductions within the first week. The use of the 3D navigation template significantly improved surgical access, enhancing safety and minimizing complications. Conclusions: The 3Dp-IFT technique represents a significant advancement in the minimally invasive removal of M3M by allowing precise access to critical anatomical areas while minimizing bone loss and postoperative complications. This approach is particularly beneficial for complex cases involving M3M near the IAN, thereby improving surgical safety and patient outcomes.