Permafrost soils store nearly half of global soil carbon (C), and therefore permafrost thawing could lead to large amounts of greenhouse gas emissions via decomposition of soil organic matter. When ice-rich permafrost thaws, it creates a localized surface subsidence called thermokarst terrain, which changes the soil microenvironment. We used soil profile CO2 measurements to understand the response of belowground C emissions for different soil depths from upland tundra as a result of permafrost thaw and thermokarst development. We established sites in central Alaska, where permafrost thaw and thermokarst development had been monitored for the past 2 decades. Cumulative growing season CO2production averaged for 3 years (2005–2007) ranged from 177 to 270 g CO2-C m−2 and was lowest in the least disturbed moist acidic tundra and highest where thawing of permafrost and thermokarst was most pronounced. We were able to explain 55% of variability in growing season soil CO2 production using surface subsidence, soil temperature, and site differences. This was likely a direct effect of permafrost thaw and thermokarst development and an indirect effect of changes in microsite soil temperature and surface moisture content, which stimulated soil organic matter decomposition and root respiration. We also observed unusually high CO2 concentrations in the early growing season, which may be attributable to trapped CO2 within air pockets in the frozen soil. Taken together, these results supported the projection that permafrost thaw and thermokarst development will increase belowground carbon emissions in the upland tundra.