The hyperarid Atacama Desert is one of the driest and oldest deserts on Earth, rendering it a valuable climate archive. However, unraveling its past climate is particularly challenging and the few studied paleoclimate records of the region reveal strong temporal and spatial variabilities. To enhance our understanding of these dynamics we investigated a sedimentary record in the Yungay valley located in the southern hyperarid Atacama Desert. We employed paleomagnetic and radiocarbon dating, and for the first time for Atacama Desert sediments, a meteoric 10Be/9Be based method for determining the depositional age. The respective 4.20 m deep profile comprises a lower alluvial fan deposit with a maximum age of 3.8 ± 0.8 Ma, and an upper 1.84 m thick clay pan deposit that has accumulated over the last 19 ka. Different proxies including grain size, salt concentration, and elemental composition indicate an aridity increase around 2.3 Ma ago and repeated dry and wet phases during the late Pleistocene and the Holocene. The latter climatic shifts can be assigned to variabilities of the South American Summer Monsoon and El Niño Southern Oscillation with moisture sources from the Atlantic and the Pacific Ocean, respectively. This study provides deeper insights into the heterogeneous climate of the hyperarid Atacama Desert and underlines the importance of interdisciplinary investigations to decipher climate systems and their effect on potential habitable regions in such an extreme environment.