Warmer temperatures and elevated atmospheric CO2 concentrations over the last several decades have been credited with increasing vegetation activity and photosynthetic uptake of CO2 from the atmosphere in the high northern latitude ecosystems: the boreal forest and Arctic tundra. At the same time, fire frequency and severity are increased, and some regions of the boreal forest show signs of stress due to drought or insect disturbance. The recent trends in net carbon balance of these ecosystems, across heterogeneous disturbance patterns, and the future implications of these changes are unclear. Here we examine CO2 fluxes from northern boreal and tundra from 1986 to 2012 estimated from two inverse models (RIGC and Jena), both using measured atmospheric CO2 concentrations and wind-fields from interannually variable reanalysis. In the arctic zone, the latitude region above 60°N excluding Europe (10° W–63° E), neither model finds a significant long-term trend in annual CO2 balance. The boreal zone, the latitude region from approximately 50° N to 60° N, again excluding Europe, absorbed an extra 8–11 Tg C yr−1 over the period from 1986 to 2006, resulting in an annual CO2 sink in 2006 that was 170–230 Tg C larger than in 1986. This same trend appears to continue through 2012 as well. In both latitudinal zones, the seasonal amplitude of monthly CO2 fluxes increased due to increased uptake in summer, and in the arctic zone, also due to increased fall CO2 release. Both models showed a seasonal flux amplitude increase of nearly 1 % yr−1 in the arctic zone, over twice the trend in the boreal zone fluxes. These findings suggest that the boreal zone has been maintaining and likely increasing CO2 sink strength over this period, despite browning trends in some regions, changes in fire frequency and land use. Meanwhile the arctic zone shows increased summer CO2 uptake, consistent with strong greening trends, is offset by increased fall CO2 release, resulting in a net neutral trend in annual fluxes. The inversion fluxes from the arctic and boreal zones covering the permafrost regions showed no indication of a large-scale positive climate-carbon feedback caused by warming temperature on high northern latitude terrestrial CO2 fluxes as of 2012.