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Although present‐day precipitation variability in the southern Altiplano and adjacent Andean margins (15–25°S) is well understood, past drivers and mechanisms remain little‐explored. We analyzed the pollen assemblages of 31 fossil rodent middens to reconstruct precipitation change during the most recent millennium in the highlands of the Atacama Desert (22°S), on the western foothills of the Altiplano. Variations in low and high elevation pollen types reveal reduced (increased) precipitation between 930 and 550 BP (510 and 440 BP) (BP = before present; taken as Common Era 1950). Variable pollen assemblages prevailed from 390 to 90 BP, followed by a drying trend that persists until present times. Similarities with proxy records from the Altiplano, the tropical Andes and the equatorial Pacific suggest that centennial‐scale wet/dry phases in the Atacama highlands were associated with changes in the strength of the South American monsoon system, most likely influenced by changes akin to modern El Niño Southern Oscillation variability. Plain Language Summary: Fossilized rodent middens are able to preserve plant remains for millennia, representing glimpses of ancient vegetation and climates. Pollen recovered from 31 fossil middens in the Atacama Desert in northern Chile allowed us to reconstruct vegetation and rainfall changes over the most recent millennium. Upslope shifts of low elevation pollen types in middens dated between 930 and 550 years before the present (BP; taken as Common Era 1950) indicates dryer conditions, while downslope shifts of high elevation types suggest wetter climates between 510 and 440 BP. We interpret these dry/wet phases as resulting from changes in regional precipitation associated with the strength of the South American summer monsoon system. A comparison of our midden record with precipitation reconstructions from the Altiplano, the tropical Andes and the equatorial Pacific suggests a pattern of variability similar to that imposed by El Niño/La Niña today. Our reconstruction further suggests that the drivers controlling present‐day precipitation variability may have also influenced decade‐to‐century‐long trends over the last 1,000 years, with the implication that future long‐term changes in El Niño Southern Oscillation behavior will more likely impact precipitation regimes in Atacama Desert and Altiplano. Key Points: Pollen analysis of fossil rodent middens from the Atacama Desert allows reconstructing precipitation trends over the last 1,100 yearsShifts in key pollen types suggest relatively dry conditions during the first half of the last millenniumA tropical driving mechanism is suggested by similarities with records from the Altiplano, the tropical Andes and the equatorial Pacific [ABSTRACT FROM AUTHOR]