Recent warming in the Arctic, which has been amplified during the winter^1-3, greatly enhances microbial decomposition of soil organic matter and subsequent release of carbon dioxide (CO₂)⁴. However, the amount of CO₂ released in winter is highly uncertain and has not been well represented by ecosystem models or by empirically-based estimates^5,6. Here we synthesize regional in situ observations of CO₂ flux from arctic and boreal soils to assess current and future winter carbon losses from the northern permafrost domain. We estimate a contemporary loss of 1662 Tg C yr^-1 from the permafrost region during the winter season (October through April). This loss is greater than the average growing season carbon uptake for this region estimated from process models (-1032 Tg C yr^-1). Extending model predictions to warmer conditions in 2100 indicates that winter CO₂ emissions will increase 17% under a moderate mitigation scenario-Representative Concentration Pathway (RCP) 4.5-and 41% under business-as-usual emissions scenario-RCP 8.5. Our results provide a new baseline for winter CO₂ emissions from northern terrestrial regions and indicate that enhanced soil CO₂ loss due to winter warming may offset growing season carbon uptake under future climatic conditions.