Abstract This study develops a novel general framework to project the permafrost fate with rigorous uncertainty quantification to assess dominant sources. Borehole temperature records from three sites in the Russian western Arctic are used to constrain the uncertainty of a high-fidelity freeze-thaw model. Projections from 9 Global Climate Models (GCM) are stochastically downscaled to generate future trajectories of surface ground heat flux. Under the two emission scenarios SSP2-4.5 and SSP5-8.5, the projected average thawing depths by 2100 vary from 0.4 to 14.4 m or 2.1 to 17.7 m, and the increase in the top 10 m average temperature from 2015 to 2100 is 1.2–2.7°C or 1.9–3.0°C. The results show that the freeze-thaw model uncertainty can sometimes dominate over that of GCM outputs, calling for site-specific information to improve model accuracy. The framework is applicable for understanding permafrost degradation and related uncertainties at larger scales.