The process and timing of skull removal remains poorly understood by researchers. New archaeological and skeletal analysis from two skeletons from the early Pre‐Pottery Neolithic (PPNA) site of Tell Qaramel, northern Syria, highlights that Neolithic villagers used stone tools to physically decapitate the dead. Drawing upon cutmarks on the axis and the mandible from a primary and a secondary burials, we employed a scanning electron microscope to document how Neolithic people cut the ligament and its surrounding connecting tissues that bind the cranium with the bones of axis and the mandible. The position of the cutmarks, especially at the top of the odontoid process of the axis, illustrates the complexities of intentional skull removal. From these and associated burial data, we illustrate that Levantine Neolithic people had specific practical codes for the sequence of skull removal, but given variation in the decomposition of the human body, at times villagers had to use flint tools for skull removal. This study provides evidence of some of the World's earliest examples of intentional decapitation within human communities. This article is protected by copyright. All rights reserved.