Releases of the greenhouse gases carbon dioxide (CO2) and methane (CH4) from thawing permafrost are expected to be among the largest feedbacks to climate from arctic ecosystems. However, the current net carbon (C) balance of terrestrial arctic ecosystems is unknown. Recent studies suggest that these ecosystems are sources, sinks, or approximately in balance at present. This uncertainty arises because there are few long-term continuous measurements of arctic tundra CO2 fluxes over the full annual cycle. Here, we describe a pattern of CO2 loss based on the longest continuous record of direct measurements of CO2 fluxes in the Alaskan Arctic, from two representative tundra ecosystems, wet sedge and heath tundra. We also report on a shorter time series of continuous measurements from a third ecosystem, tussock tundra. The amount of CO2 loss from both heath and wet sedge ecosystems was related to the timing of freeze-up of the soil active layer in the fall. Wet sedge tundra lost the most CO2 during the anomalously warm autumn periods of September–December 2013–2015, with CH4 emissions contributing little to the overall C budget. Losses of C translated to approximately 4.1 and 1.4% of the total soil C stocks in active layer of the wet sedge and heath tundra, respectively, from 2008 to 2015. Increases in air temperature and soil temperatures at all depths may trigger a new trajectory of CO2 release, which will be a significant feedback to further warming if it is representative of larger areas of the Arctic.