A paleoradiographic survey of funerary bundles (fardos) from a Late Intermediate Period (1000 AD–1472 AD) cemetery in Sector 3 of the site of Pachacamac, Peru, demonstrated that 15 out of 61 individuals had had their head removed when the body was in an advanced state of skeletonization/mummification. Detailed analysis of the field report, the fardos themselves, and X-rays and computed tomography scans of the fardos suggested that nine of these individuals were potential candidates for head removal in antiquity. Of those nine, six appeared to be clear examples of this practice. The analysis of multiple lines of evidence suggests that the use of this cemetery was complex, as part of a dynamic mortuary program that involved exposing the body for varying lengths of time and repeated excavations for new interments when earlier burials were encountered. We conclude that these heads were removed from funerary bundles when graves were being dug for subsequent burials and the specific identity of the bundled individual had been lost. When considered within the abundant archaeological record of decapitation in the Pre-Hispanic Andes, as well as ethnohistoric accounts, this pattern is consistent with reported retrieval of heads as material manifestations of ancestors. However, when placed within the broader context of contemporary sites from the Central and Southern Coast, it is clear that specific cultural motivations may have varied through space and time.