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Abstract Paleoclimate reconstructions from the Holocene are important for defining baseline conditions in order to interpret and contextualize the effects of modern climate change. Such records are particularly lacking for Siberia, a region that represents ~ 50% of the Arctic. In addition, the majority of proxy-based paleoclimate reconstructions for the Holocene represent mean annual conditions, and few quantify winter temperature, which is particularly important for predicting the effects of global warming in Arctic environments. Here we provide the first quantitative proxy reconstruction of precipitation and temperature for both summer and winter for 3000 years ago via novel high-resolution intra-annual carbon and oxygen isotope measurements across annual growth rings of fossil wood mummified within the permafrost of far northeastern Siberia. We found that the site experienced greater precipitation year-round (~ 10% increase in summer and ~ 30% increase in winter), cooler summer temperatures, and warmer winter temperatures, compared with today. Our findings indicate that warmer winter temperatures (+ 3.0 °C above early twentieth century values) in the Arctic 3000 years ago drove higher mean annual temperature by up to 1 °C, despite the existence of cooler summers, a similar phenomenon to what is observed within today’s Arctic environments, and past intervals of extreme global warmth.