Rapid permafrost degradation and peatland expansion occurred in Eurasia during the Early Holocene and may be analogous to the region’s response to anthropogenic warming. Here we present a 230Th-dated, multiproxy speleothem record with subdecadal sampling resolution from Kyok-Tash Cave, at the modern permafrost margin in the northern Altai Mountains, southwestern Siberia. Stalagmite K4, covering the period 11,400 to 8,900 years before present, indicates an absence of stable permafrost within three centuries of the Younger Dryas termination. Between 11,400 and 10,400 years ago, speleothem δ18O is antiphased between the Altai and Ural ranges, suggesting a reorganization of the westerly wind systems that led to warmer and wetter winters over West Siberia and Altai, relative to the zonally adjacent regions of Northern Eurasia. At the same time, there is evidence of peak permafrost degradation and peatland expansion in West Siberia, consistent with the interpreted climate anomaly. Based on these findings, we suggest that modern permafrost in Eurasia is sensitive to feedbacks in the ocean-cryosphere system, which are projected to alter circulation regimes over the continent.