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 0.36 (-620, 652) Tg CO₂-C y^-1, 38 (21, 53) Tg CH₄-C y^-1, and 0.62 (0.03, 1.2) Tg N₂O-N y^-1 to the atmosphere throughout the period. While the region was a net source of CH₄ and N₂O, the CO₂ budget was near neutral with large uncertainties. Terrestrial ecosystems remained a CO₂ sink, but emissions from fire disturbances and inland waters largely offset the sink in vegetated ecosystems. Including lateral fluxes, the permafrost region was a net source of C and N, releasing 136 (-517, 821) Tg C y^-1 and 3.2 (1.9, 4.8) Tg N y^-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.