Fire is an important factor controlling the composition and thickness of the organic layer in the black spruce forest ecosystems of interior Alaska. Fire that burns the organic layer can trigger dramatic changes in the underlying permafrost, leading to accelerated ground thawing within a relatively short time. In this study, we addressed the following questions. (1) Which factors determine post-fire ground temperature dynamics in lowland and upland black spruce forests? (2) What levels of burn severity will cause irreversible permafrost degradation in these ecosystems? We evaluated these questions in a transient modeling–sensitivity analysis framework to assess the sensitivity of permafrost to climate, burn severity, soil organic layer thickness, and soil moisture content in lowland (with thick organic layers, ~80 cm) and upland (with thin organic layers, ~30 cm) black spruce ecosystems. The results indicate that climate warming accompanied by fire disturbance could significantly accelerate permafrost degradation. In upland black spruce forest, permafrost could completely degrade in an 18 m soil column within 120 years of a severe fire in an unchanging climate. In contrast, in a lowland black spruce forest, permafrost is more resilient to disturbance and can persist under a combination of moderate burn severity and climate warming.