Human sacrifice became a common cultural trait during the advanced phases of Mesoamerican civilizations. This phenomenon, influenced by complex religious beliefs, included several practices such as decapitation, cranial deformation, and the use of human cranial bones for skull mask manufacturing. Archaeological evidence suggests that all of these practices required specialized knowledge of skull base and upper cervical anatomy. The authors conducted a systematic search for information on skull base anatomical and surgical knowledge among Mesoamerican civilizations. A detailed exposition of these results is presented, along with some interesting information extracted from historical documents and pictorial codices to provide a better understanding of skull base surgical practices among these cultures. Paleoforensic evidence from the Great Temple of Tenochtitlan indicates that Aztec priests used a specialized decapitation technique, based on a deep anatomical knowledge. Trophy skulls were submitted through a stepwise technique for skull mask fabrication, based on skull base anatomical landmarks. Understanding pre-Columbian Mesoamerican religions can only be realized by considering them in their own time and according to their own perspective. Several contributions to medical practice might have arisen from anatomical knowledge emerging from human sacrifice and decapitation techniques.