AbstractPermafrost thaw in northern peatlands causes collapse of permafrost peat plateaus and thermokarst bog development, with potential impacts on atmospheric greenhouse gas exchange. Here, we measured methane and carbon dioxide fluxes over 3 years (including winters) using static chambers along two permafrost thaw transects in northwestern Canada, spanning young (~30 years since thaw), intermediate and mature thermokarst bogs (~200 years since thaw). Young bogs were wetter, warmer and had more hydrophilic vegetation than mature bogs. Methane emissions increased with wetness and soil temperature (40 cm depth) and modelled annual estimates were greatest in the young bog during the warmest year and lowest in the mature bog during the coolest year (21 and 7 g C‐CH4 m−2 year−1, respectively). The dominant control on net ecosystem exchange (NEE) in the mature bog (between +20 and −54 g C‐CO2 m−2 year−1) was soil temperature (5 cm), causing net CO2 loss due to higher ecosystem respiration (ER) in warmer years. In contrast, wetness controlled NEE in the young and intermediate bogs (between +55 and −95 g C‐CO2 m−2 year−1), where years with periodic inundation at the beginning of the growing season caused greater reduction in gross primary productivity than in ER leading to CO2 loss. Winter fluxes (November–April) represented 16% of annual ER and 38% of annual CH4 emissions. Our study found NEE of thermokarst bogs to be close to neutral and rules out large CO2 losses under current conditions. However, high CH4 emissions after thaw caused a positive net radiative forcing effect. While wet conditions favouring high CH4 emissions only persist for the initial young bog period, we showed that continued climate warming with increased ER, and thus, CO2 losses from the mature bog can cause net positive radiative forcing which would last for centuries after permafrost thaw.