This study analyzes the earliest known case of surgical extraction of the lower third molars, observed in a cranial series from Pucará de Tilcara fortress (15th–16th centuries AD), northwestern Argentina, excavated in 1908–1910. Crania were transported to the Kunstkamera in 1910 under an exchange project. Traces of dental surgery were registered in the mandible of a male aged ~40. Both third molars had been extracted after the removal of soft tissues and parts of the alveoli. Teeth were extracted by scraping alveolar walls with semicircular movements. The results of scanning electron microscopy, X-ray fluorescence, and X-ray microanalysis suggest that a stone tool was used. The results of macroscopic and CT analysis suggest that the surgery was motivated by the exacerbation of chronic periodontal disease and probably by caries. The left third molar was extracted without complications 2–3 months before the individual’s death. On the right side, the pathological process continued, culminating in osteomyelitis and its complications. The surgeon’s skill notwithstanding, the extraction of the right third molar did not cure the patient, who died, apparently following the destructive stage of acute osteomyelitis complicated by orofacial phlegmon. Our findings suggest that the level of dental surgery practiced in the Inca Empire was ahead of the diagnostic expertise.