Climate warming in high-latitude regions is thawing carbon-rich permafrost soils, which can release carbon to the atmosphere and enhance climate warming. Using a coupled model of long-term peatland dynamics (Holocene Peat Model, HPM-Arctic), we quantify the potential loss of carbon with future climate warming for six sites with differing climates and permafrost histories in Northwestern Canada. We compared the net carbon balance at 2100 CE resulting from new productivity and the decomposition of active layer and newly-thawed permafrost peats under RCP8.5 as a high-end constraint. Modeled net carbon losses ranged from -3.0 kg C m-2 (net loss) to +0.1 kg C m-2 (net gain) between 2015 to 2100. Losses of newly thawed permafrost peat comprised 0.2 to 25% (median: 1.6%) of “old” C loss, which were related to the residence time of peat in the active layer before being incorporated into the permafrost, peat temperature, and presence of permafrost. The largest C loss was from the permafrost-free site, not from permafrost sites. C losses were greatest from depths of 0.2 – 1.0 m. New C added to the profile through net primary productivity between 2015-2100 offset ~40% to >100% of old C losses across the sites. Differences between modeled active layer deepening and flooding following permafrost thaw resulted in very small differences in net C loss by 2100, illustrating the important role of present-day conditions and permafrost aggradation history in controlling net C loss.