The northern permafrost region has been projected to shift from a net sink to a net source of carbon under global warming. However, estimates of the contemporary net greenhouse gas (GHG) balance and budgets of the permafrost region remain highly uncertain. Here, we construct the first comprehensive bottom‐up budgets of CO2, CH4, and N2O across the terrestrial permafrost region using databases of more than 1000 in situ flux measurements and a land cover‐based ecosystem flux upscaling approach for the period 2000–2020. Estimates indicate that the permafrost region emitted a mean annual flux of 12 (−606, 661) Tg CO2–C yr−1, 38 (22, 53) Tg CH4–C yr−1, and 0.67 (0.07, 1.3) Tg N2O–N yr−1 to the atmosphere throughout the period. Thus, the region was a net source of CH4 and N2O, while the CO2 balance was near neutral within its large uncertainties. Undisturbed terrestrial ecosystems had a CO2 sink of −340 (−836, 156) Tg CO2–C yr−1. Vertical emissions from fire disturbances and inland waters largely offset the sink in vegetated ecosystems. When including lateral fluxes for a complete GHG budget, the permafrost region was a net source of C and N, releasing 144 (−506, 826) Tg C yr−1 and 3 (2, 5) Tg N yr−1. Large uncertainty ranges in these estimates point to a need for further expansion of monitoring networks, continued data synthesis efforts, and better integration of field observations, remote sensing data, and ecosystem models to constrain the contemporary net GHG budgets of the permafrost region and track their future trajectory. Plain Language Summary A quarter of the northern hemisphere is underlain by a permanently frozen ground called permafrost. This ground contains large amounts of carbon and nitrogen, making the permafrost region the largest terrestrial carbon and nitrogen pool on Earth. Due to unprecedented warming, permafrost thaws and reshapes landscapes, impacting their hydrology and biogeochemical cycling. This has the potential to increase the release of greenhouse gases such as carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) to the atmosphere, impacting the global climate. Although presumably crucial for the global carbon cycle, the role of the permafrost region in the global carbon budget is unknown. We present comprehensive budgets of CO2, CH4, and N2O by key permafrost land cover types over the period 2000–2020 across the northern permafrost region. Estimates indicate that the permafrost region was emitting GHGs throughout the period. While the region was a source of methane and nitrous oxide, the carbon dioxide budget was near neutral with large uncertainties. Carbon dioxide emissions from wildfires and inland waters largely offset the sink in vegetated ecosystems. Uncertainties in estimates would be narrowed by increasing the number of in situ flux measurements in various ecosystems, sharpening ecosystem classifications, and integrating fluxes from disturbances. Key Points The region emitted 12 (−606, 661) Tg CO2–C yr−1, 38 (22, 53) Tg CH4–C yr−1, and 0.67 (0.07, 1.3) Tg N2O–N yr−1 to the atmosphere between 2000 and 2020 Based on the above, terrestrial ecosystems remained a CO2 sink, but emissions from fires and inland waters largely offset the sink in vegetated ecosystems When also including lateral fluxes, the complete C and N budgets of the permafrost region result in net sources of 144 (−506, 826; including CO2 and CH4) Tg C yr−1 and 3 (2, 5) Tg N yr−1