Paleoparasitology offers a window into prehistoric parasite faunas, and through studying time-series of parasite assemblages it may be possible to observe how parasites responded to past environmental or climate change, or habitat loss (host decline). Here, we use DNA metabarcoding to reconstruct parasite assemblages in twenty-eight ancient rodent middens (or paleomiddens) from the central Atacama Desert in northern Chile. The paleomiddens span the last 50,000 years, and include middens deposited before, during and after the Central Andean Pluvial Event (CAPE; 17.5–8.5 ka BP). The CAPE was a period of increased precipitation and vegetation change, which we also demonstrate was associated with changes in local rodent taxa. Thirteen parasite taxa (including lice, mites, ticks, nematodes and coccidians) were identified from the middens, nine of which were likely derived from rodent hosts and four from alternative (insect or avian) hosts. The former are consistent with parasites known to infect South American rodent hosts. At our conservative level of high taxonomic rank assignment, the parasites appear to have been resilient to the major perturbations in climate and host taxa associated with the CAPE, and finer taxonomic resolution would be required to detect whether any species turnover occurred within the identified parasite groups. Rodent paleomiddens are fast becoming an unrivaled source of genomic data that can be used to reconstruct past ecosystem change on multiple taxonomic, temporal and spatial scales providing new insights into ecological responses to global change.